Contacts of the helix formed by residues 287 - 309 (chain A) in PDB entry 4LOU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A HIS* 2.9 15.7 + - - +
285A GLY 3.5 0.8 - - - -
286A GLY* 1.3 75.2 - - - +
288A ILE* 1.3 70.1 + - - +
289A THR* 2.9 16.2 + - - +
290A LYS* 2.8 43.2 + - + +
291A TRP* 2.9 22.2 + - - +
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A PHE* 4.1 15.7 - - + -
98A ARG* 3.8 29.4 - - + +
99A LYS* 3.9 35.9 - - + +
286A GLY 3.2 7.3 + - - -
287A ASN* 1.3 74.5 - - - +
289A THR* 1.3 69.6 + - - +
291A TRP* 3.8 4.9 - - - +
292A VAL* 2.9 39.3 + - + +
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Residues in contact with THR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASN* 2.9 13.9 + - - -
288A ILE* 1.3 84.8 - - - +
290A LYS* 1.3 67.4 + - + +
292A VAL* 3.4 4.0 + - - +
293A LEU* 3.0 43.5 + - + +
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Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A VAL* 3.7 19.3 + - + +
284A HIS* 3.6 33.3 + - + +
287A ASN* 2.8 26.4 + - + +
289A THR* 1.3 73.8 - - + +
291A TRP* 1.3 53.2 + - - +
293A LEU* 3.3 8.8 + - - +
294A MET* 2.8 35.9 + - - +
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Residues in contact with TRP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 4.0 18.5 - + - -
98A ARG* 3.2 55.9 - - - -
281A HIS* 4.3 16.2 - + - -
284A HIS* 3.1 45.0 + + + +
286A GLY* 4.2 11.0 - - - -
287A ASN 2.9 14.7 + - - +
288A ILE* 3.8 5.6 - - - +
290A LYS* 1.3 74.0 - - - +
292A VAL* 1.3 61.3 + - - +
294A MET* 3.1 18.7 + - + +
295A GLY* 2.8 26.2 + - - -
350A SER 3.3 28.5 + - - -
351A GLY* 4.7 7.2 - - - -
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 3.1 36.1 - - + +
94A TYR* 4.2 9.4 - - + +
95A PHE* 3.5 40.4 - - + +
98A ARG* 4.9 2.9 - - + -
288A ILE* 2.9 35.1 + - + +
289A THR* 4.0 4.3 - - - +
291A TRP* 1.3 70.8 - - - +
293A LEU* 1.3 66.5 + - + +
295A GLY* 3.2 2.9 + - - -
296A GLY 3.1 17.8 + - - -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 4.3 18.6 - - - +
289A THR* 3.0 35.9 + - + +
290A LYS* 3.5 7.4 - - - +
292A VAL* 1.3 77.9 - - + +
294A MET* 1.3 65.2 + - - +
296A GLY* 3.2 3.0 + - - +
297A ALA* 3.0 22.6 + - - +
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Residues in contact with MET 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 5.0 0.2 - - + -
280A LEU* 3.5 40.4 - - + +
283A VAL* 3.7 27.1 - - + -
284A HIS* 3.8 8.7 - - + -
290A LYS 2.8 21.2 + - - +
291A TRP* 3.1 30.7 + - + +
293A LEU* 1.3 72.9 - - - +
295A GLY* 1.3 61.8 + - - +
297A ALA* 3.3 7.8 + - + +
298A ILE* 3.1 45.8 + - + +
350A SER* 4.5 5.4 - - - +
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Residues in contact with GLY 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ALA* 3.4 7.1 - - - +
94A TYR* 3.2 40.6 - - - -
291A TRP 2.8 11.5 + - - -
292A VAL 3.5 4.5 - - - -
293A LEU 3.1 0.2 - - - -
294A MET* 1.3 74.4 - - - +
296A GLY* 1.3 60.0 + - - +
297A ALA 3.1 1.6 - - - -
298A ILE* 3.3 3.6 + - - +
299A GLY 2.9 24.9 + - - -
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Residues in contact with GLY 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 4.1 2.1 - - - -
87A ALA* 3.1 28.6 - - - +
90A ALA* 3.8 3.6 - - - -
91A MET* 3.3 25.2 - - - +
292A VAL 3.1 11.7 + - - -
293A LEU 3.2 2.8 + - - -
295A GLY* 1.3 75.0 - - - +
297A ALA* 1.3 56.8 + - - +
299A GLY 4.0 0.7 - - - -
300A GLY* 3.1 20.1 + - - -
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 3.8 16.3 - - + -
293A LEU 3.0 13.1 + - - +
294A MET* 3.5 13.2 - - + +
295A GLY 3.1 0.2 - - - -
296A GLY* 1.3 76.4 - - - +
298A ILE* 1.3 65.7 + - + +
300A GLY* 3.3 2.3 + - - -
301A LEU* 2.9 22.2 + - - +
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 3.8 5.2 - - - +
143A MET* 3.6 21.5 - - + -
280A LEU* 4.5 7.6 - - + -
294A MET* 3.1 30.2 + - + +
295A GLY 3.6 5.8 - - - +
297A ALA* 1.3 77.3 - - + +
299A GLY* 1.3 64.5 + - - +
301A LEU* 2.9 19.8 + - - +
302A CYS* 3.0 15.3 + - - -
346A LEU* 4.0 31.0 - - + +
347A CYS* 4.1 15.3 - - - -
350A SER* 3.7 29.2 - - - -
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Residues in contact with GLY 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER* 3.1 16.4 - - - -
90A ALA* 3.8 18.4 - - - +
141A GLY 4.7 0.3 - - - +
143A MET* 4.0 18.3 - - - +
295A GLY 2.9 18.6 + - - -
298A ILE* 1.3 72.7 - - - +
300A GLY* 1.3 55.7 + - - +
302A CYS* 3.2 3.5 + - - +
303A GLY 2.8 25.5 + - - -
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Residues in contact with GLY 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.3 50.0 - - - -
86A SER* 4.1 0.7 - - - -
87A ALA 3.9 1.6 - - - +
296A GLY 3.1 14.1 + - - -
297A ALA 3.7 0.2 - - - -
298A ILE 3.2 0.2 - - - -
299A GLY* 1.3 71.5 - - - +
301A LEU* 1.3 60.7 + - - +
303A GLY 3.4 0.2 + - - -
304A LEU* 2.9 30.8 + - - +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 3.8 4.6 - - + -
297A ALA 2.9 12.5 + - - +
298A ILE* 2.9 12.0 + - - +
300A GLY* 1.3 76.2 - - - +
302A CYS* 1.3 60.9 + - - +
304A LEU* 3.3 16.0 + - + +
305A LEU* 3.0 54.2 + - + +
342A ILE* 6.5 1.3 - - + -
343A THR* 5.5 6.5 - - + -
346A LEU* 4.0 26.7 - - + -
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Residues in contact with CYS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLY 3.5 18.4 - - - +
143A MET* 3.9 9.4 - - - -
144A VAL* 4.2 8.5 - - - -
298A ILE* 3.0 21.1 + - - -
299A GLY 3.2 6.7 + - - +
301A LEU* 1.3 77.5 - - - +
303A GLY* 1.3 60.0 + - - +
304A LEU 3.0 1.8 - - - -
305A LEU* 3.3 4.7 + - - +
306A GLY* 2.8 25.3 + - - -
313A SER* 3.1 19.2 + - - +
343A THR* 5.3 7.2 - - - -
346A LEU* 6.4 0.7 - - - -
347A CYS* 3.4 33.2 - - - -
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Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 3.7 13.0 + - - -
68A LEU* 5.9 0.3 - - - +
82A ALA* 3.8 20.1 - - - +
86A SER* 3.1 29.6 + - - -
141A GLY 4.1 2.4 + - - -
142A GLY 5.1 0.4 - - - -
299A GLY 2.8 14.1 + - - -
300A GLY 3.7 0.7 - - - -
302A CYS* 1.3 72.9 - - - +
304A LEU* 1.3 60.9 + - - +
306A GLY* 3.7 7.9 + - - -
307A PHE* 3.8 5.0 + - - +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.3 45.7 - - + +
82A ALA* 4.5 6.3 + - + -
83A PHE* 4.3 12.8 - - + +
300A GLY 2.9 18.2 + - - +
301A LEU* 3.3 18.6 - - + +
302A CYS 3.0 0.2 - - - -
303A GLY* 1.3 73.6 - - - +
305A LEU* 1.3 58.3 + - + +
306A GLY 3.0 3.8 - - - -
307A PHE* 2.8 27.2 + - - +
308A VAL* 3.2 26.1 + - + +
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LEU* 3.0 37.9 + - + +
302A CYS* 3.7 7.4 - - - +
304A LEU* 1.3 82.9 - - + +
306A GLY* 1.3 57.7 + - - +
307A PHE 3.0 0.7 - - - -
308A VAL* 3.8 17.7 - - + -
309A ALA* 2.8 41.2 + - + +
312A THR* 3.5 27.8 - - + +
313A SER* 4.0 6.7 - - - -
343A THR* 3.9 25.4 - - + -
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Residues in contact with GLY 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 5.9 2.0 - - - -
65A MET* 5.8 3.8 - - - +
68A LEU* 6.2 0.2 - - - -
302A CYS 2.8 17.5 + - - -
303A GLY* 3.9 7.9 - - - -
304A LEU 3.0 0.8 - - - -
305A LEU* 1.3 76.1 - - - +
307A PHE* 1.3 57.4 + - - +
310A PRO* 3.9 19.8 - - - +
313A SER* 4.0 11.4 - - - -
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A MET* 5.7 3.6 - - + -
68A LEU* 3.4 32.3 - - + -
75A TYR* 4.1 16.2 - + - -
78A LEU* 3.3 35.9 - - + -
79A LEU* 3.8 11.2 - - + -
82A ALA* 4.7 6.3 - - + -
303A GLY 3.8 5.5 + - - +
304A LEU 2.8 10.4 + - - +
306A GLY* 1.3 81.3 - - - +
308A VAL* 1.3 73.6 + - + +
309A ALA 3.6 1.1 + - - -
310A PRO* 4.3 8.7 - - - +
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 3.9 13.0 - - - +
79A LEU* 3.8 19.7 - - + -
304A LEU* 3.2 24.4 + - + +
305A LEU* 3.9 19.5 - - + +
307A PHE* 1.3 98.1 - - + +
309A ALA* 1.3 64.7 + - + +
310A PRO* 3.9 2.7 - - - +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 2.8 14.3 + - + +
308A VAL* 1.3 88.0 - - + +
310A PRO* 1.3 57.2 - - - +
311A ALA* 3.1 2.9 - - - -
312A THR* 2.7 51.7 + - + +
335A PHE* 4.7 13.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il