Contacts of the helix formed by residues 299 - 316 (chain A) in PDB entry 3EGC
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 PRO 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A SER* 4.0 12.3 - - - +
297A GLU* 4.2 2.9 - - + +
298A GLN* 1.4 81.7 - - + +
300A THR* 1.3 65.0 + - - +
301A ARG 3.4 2.2 - - - -
302A ARG* 3.1 19.0 + - + -
303A ILE* 2.9 25.9 + - + +
326A LEU* 3.7 25.1 - - + -
327A GLN 3.3 26.9 - - - +
328A THR* 4.3 4.7 - - + -
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.6 42.2 - - + +
84A GLU* 2.4 44.8 + - - +
85A VAL* 3.5 11.1 - - - +
281A ASP* 5.5 0.9 - - - +
298A GLN* 2.9 21.7 + - + +
299A PRO* 1.3 72.3 - - - +
301A ARG* 1.3 73.4 + - - +
303A ILE* 3.3 10.8 + - - +
304A GLY 3.2 16.3 + - - -
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 3.5 46.8 + - - +
87A SER* 4.4 1.1 - - - +
88A GLY* 3.4 16.8 - - - +
299A PRO 3.4 0.6 - - - -
300A THR* 1.3 83.2 + - - +
302A ARG* 1.3 57.5 + - - +
304A GLY 3.2 2.4 + - - -
305A GLN* 2.9 26.5 + - - +
78B GLU* 2.4 50.0 + - - +
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PRO* 3.1 20.4 + - + +
301A ARG* 1.3 74.2 - - - +
303A ILE* 1.3 66.0 + - - +
305A GLN* 3.4 23.0 + - - -
306A GLU* 2.6 60.9 + - + +
309A ARG* 4.2 7.3 - - - +
324A MET* 5.5 2.6 - - - +
326A LEU* 3.8 20.6 - - + +
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Residues in contact with ILE 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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81A PHE* 4.4 20.0 - - + -
85A VAL* 4.3 9.0 - - + -
152A VAL* 3.9 19.5 - - + -
153A ASN* 4.8 4.0 - - - +
164A VAL* 3.7 27.4 - - + +
165A LEU 5.0 1.6 - - - +
166A SER* 3.5 27.8 - - - +
298A GLN* 4.6 0.2 - - - +
299A PRO* 2.9 31.5 + - + +
300A THR* 3.4 12.3 - - - +
301A ARG 3.2 0.2 - - - -
302A ARG* 1.3 75.6 - - - +
304A GLY* 1.3 62.0 + - - +
307A ALA* 3.0 24.9 + - - +
326A LEU* 3.7 21.5 - - + -
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Residues in contact with GLY 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 3.3 30.9 - - - +
89A VAL* 3.4 25.2 - - - +
300A THR 3.2 5.1 + - - -
301A ARG 3.2 5.6 + - - -
303A ILE* 1.3 80.4 - - - +
305A GLN* 1.3 61.2 + - - +
307A ALA* 3.4 1.7 + - - +
308A MET 3.0 19.1 + - - -
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Residues in contact with GLN 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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88A GLY* 3.5 17.7 - - - +
91A SER* 6.0 1.6 + - - -
92A GLU* 3.3 35.7 + - + +
301A ARG 2.9 18.8 + - - +
302A ARG* 3.4 31.4 + - - +
304A GLY* 1.3 71.4 - - - +
306A GLU* 1.3 52.4 + - - +
308A MET 3.4 0.5 + - - -
309A ARG* 2.8 57.8 + - - +
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Residues in contact with GLU 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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164A VAL* 4.2 9.3 - - + +
302A ARG* 2.6 64.8 + - + +
303A ILE 4.1 2.0 - - - +
305A GLN* 1.3 72.6 - - - +
307A ALA* 1.3 60.8 + - - +
309A ARG* 3.1 30.2 + - - +
310A MET* 2.9 31.2 + - - +
324A MET* 3.3 41.1 - - + +
326A LEU* 4.3 3.4 - - + -
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Residues in contact with ALA 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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128A ILE* 3.8 11.2 - - + -
150A VAL* 3.6 17.6 - - + +
152A VAL* 3.4 26.9 - - + -
164A VAL* 3.5 15.8 - - + +
303A ILE 3.0 20.3 + - - +
304A GLY* 3.8 4.5 - - - +
306A GLU* 1.3 75.3 - - - +
308A MET* 1.3 58.9 + - - +
310A MET* 3.6 1.0 + - - +
311A LEU* 3.0 29.5 + - - +
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Residues in contact with MET 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 3.6 34.8 - - + -
72A LEU* 5.9 0.2 - - + -
89A VAL* 2.8 48.7 - - + +
92A GLU* 3.8 8.7 - - + -
93A ALA* 3.8 23.1 - - + +
98A TYR* 5.4 0.9 - - - -
100A VAL* 4.3 3.1 - - + -
128A ILE* 3.3 17.5 - - + +
304A GLY 3.0 17.0 + - - +
305A GLN 3.6 4.9 - - - +
307A ALA* 1.3 74.9 - - - +
309A ARG* 1.3 58.3 + - - +
311A LEU* 3.4 7.6 + - - +
312A ILE* 3.0 53.8 + - + +
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Residues in contact with ARG 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 3.4 30.9 + - - +
96A LYS* 4.0 10.2 + - - +
302A ARG* 4.2 7.7 - - - +
305A GLN* 2.8 49.5 + - - +
306A GLU* 3.1 39.9 + - - +
308A MET* 1.3 68.3 - - - +
310A MET* 1.3 66.8 + - - +
312A ILE* 3.2 7.5 + - - +
313A HIS* 3.1 36.9 + - + +
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Residues in contact with MET 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 3.4 18.6 - - + -
162A GLY* 2.5 49.4 - - - +
163A ALA 4.2 6.1 - - - +
164A VAL* 4.8 6.1 - - + -
306A GLU 2.9 20.0 + - - +
307A ALA* 3.8 5.2 - - - +
309A ARG* 1.3 74.2 - - - +
311A LEU* 1.3 61.5 + - - +
313A HIS* 3.5 10.9 + - - +
314A MET* 3.0 29.0 + - - +
320A ASN 4.0 15.3 - - - +
321A ALA* 3.9 3.6 - - - -
322A THR* 3.4 32.1 - - + +
324A MET* 5.4 8.7 - - - +
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 3.4 43.5 - - + -
126A GLY* 3.8 1.6 - - - -
127A LEU 3.7 17.9 - - - +
128A ILE* 3.8 13.7 - - + -
148A PRO* 3.7 35.4 - - + +
150A VAL* 3.6 22.4 - - + +
307A ALA 3.0 18.1 + - - +
308A MET* 3.8 9.0 - - - +
309A ARG 3.3 0.4 - - - -
310A MET* 1.3 75.8 - - - +
312A ILE* 1.3 58.3 + - - +
314A MET* 3.4 4.2 + - - +
315A ILE* 3.0 39.0 + - + +
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Residues in contact with ILE 312 (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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92A GLU* 4.5 3.1 - - + +
93A ALA* 4.9 0.7 - - - -
96A LYS* 3.6 54.1 - - + +
98A TYR* 4.1 21.1 - - + +
308A MET* 3.0 44.3 + - + +
309A ARG* 3.2 5.1 + - - +
311A LEU* 1.3 74.6 - - - +
313A HIS* 1.3 70.4 + - + +
315A ILE* 3.0 7.3 + - + +
316A GLU* 2.9 53.7 + - + +
318A THR* 5.8 0.2 - - - +
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Residues in contact with HIS 313 (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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96A LYS* 5.7 7.0 + - - -
309A ARG* 3.1 32.4 + - + +
310A MET* 3.5 11.4 - - - +
312A ILE* 1.3 79.1 - - + +
314A MET* 1.3 56.7 + - - +
317A GLY* 2.9 12.0 + - - -
318A THR* 2.7 56.4 + - - -
319A GLY* 3.4 24.0 + - - +
320A ASN 5.5 1.3 - - - +
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Residues in contact with MET 314 (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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148A PRO* 3.8 29.6 - - + +
149A ILE 3.9 14.8 - - - +
150A VAL* 3.7 22.0 - - - -
160A GLY 3.7 12.1 - - - +
310A MET* 3.0 19.8 + - - +
311A LEU* 3.6 7.0 - - - +
312A ILE 3.2 0.2 - - - -
313A HIS* 1.3 75.9 - - - +
315A ILE* 1.3 62.2 + - - +
317A GLY* 3.9 5.9 + - - -
319A GLY 3.7 7.4 - - - +
320A ASN* 4.1 4.3 - - - -
321A ALA* 3.6 46.0 - - + +
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Residues in contact with ILE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG 4.8 7.4 - - - +
70A VAL* 3.9 15.0 - - + -
98A TYR* 3.9 22.7 - - + +
125A ASP* 3.7 51.4 - - + +
148A PRO* 3.7 11.4 - - + -
311A LEU* 3.0 42.5 + - + +
312A ILE* 3.0 6.9 + - + +
314A MET* 1.3 77.9 - - - +
316A GLU* 1.3 62.0 + - + +
317A GLY 3.2 2.0 + - - -
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Residues in contact with GLU 316 (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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68A ASN* 5.3 0.5 + - - -
96A LYS* 5.4 1.9 - - - +
98A TYR* 2.6 40.0 + - - +
312A ILE* 2.9 28.2 + - - +
315A ILE* 1.3 78.3 - - + +
317A GLY* 1.3 62.9 + - - +
318A THR* 3.4 21.3 + - + +
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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
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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