Contacts of the helix formed by residues 297 - 309 (chain A) in PDB entry 4F5G
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 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLN* 2.8 21.2 + - - +
111A PRO* 4.0 20.0 - - + -
263A GLU 3.7 9.6 - - - +
264A ARG* 3.6 25.1 - - + +
265A VAL* 5.8 0.3 - - - +
293A TYR* 5.4 0.9 - - + -
296A PRO* 1.3 85.8 - - + +
298A ALA* 1.3 59.0 + - - +
299A HIS* 3.5 3.5 + - + +
300A GLY 4.3 4.5 + - - -
301A ALA 4.3 1.7 + - - -
111B PRO* 5.6 1.8 - - + -
262B ASN 3.5 6.7 - - - +
263B GLU* 3.8 11.0 - - - +
264B ARG* 3.5 8.9 - - + -
297B PRO* 3.6 31.2 - - + -
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Residues in contact with ALA 298 (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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70A GLU* 5.6 4.3 - - - +
76A LEU* 5.0 8.3 - - + -
81A LEU* 6.4 1.6 - - + -
109A GLN* 4.1 6.5 - - - +
296A PRO 3.3 1.9 + - - +
297A PRO* 1.3 72.1 - - - +
299A HIS* 1.3 67.8 + - - +
301A ALA* 3.2 4.8 + - - +
302A SER* 2.9 32.2 + - - +
262B ASN* 2.8 48.1 + - + +
263B GLU* 3.6 4.9 + - - +
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 2.6 48.4 + - + +
66A LEU* 4.5 14.1 - - + +
70A GLU* 5.9 1.7 + - - -
73A LYS* 5.4 0.6 + - - -
260A LEU* 6.0 0.2 - - + -
263A GLU* 3.5 26.5 - - + +
297A PRO* 3.5 2.5 - - + +
298A ALA* 1.3 75.6 - - - +
300A GLY* 1.3 57.7 + - - +
302A SER* 3.3 6.4 + - - -
303A VAL* 3.0 36.3 + - + +
63B GLU* 4.8 2.3 + - - -
73B LYS* 5.3 0.2 - - - -
263B GLU* 3.0 23.8 + - - +
299B HIS* 3.5 42.5 + + + -
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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
----------------------------------------------------------
260A LEU* 3.8 3.7 - - - +
263A GLU* 4.0 16.3 + - - +
265A VAL* 3.2 27.9 - - - +
297A PRO 4.3 3.0 + - - -
298A ALA 3.4 0.4 - - - -
299A HIS* 1.3 81.3 - - - +
301A ALA* 1.3 57.5 + - - +
303A VAL* 3.3 9.0 + - - +
304A VAL* 3.0 31.0 + - - +
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.2 4.9 - - + -
84A PHE* 3.6 29.9 - - + +
109A GLN* 3.2 44.0 - - + +
265A VAL* 3.8 7.9 - - + +
297A PRO 4.3 1.8 + - - -
298A ALA 3.2 4.5 + - - +
300A GLY* 1.3 73.8 - - - +
302A SER* 1.3 61.2 + - - +
304A VAL 3.2 0.5 + - - -
305A ALA* 2.9 30.7 + - - +
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Residues in contact with SER 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.6 26.5 - - - -
70A GLU* 4.7 8.5 + - - -
81A LEU* 3.8 23.1 - - - +
298A ALA* 2.9 27.2 + - - +
299A HIS* 3.6 4.0 - - - -
301A ALA* 1.3 75.8 - - - +
303A VAL* 1.3 59.0 + - - +
305A ALA* 3.5 1.4 + - - +
306A THR* 2.6 35.0 + - - -
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.9 19.3 - - + -
62A ALA* 3.9 17.9 - - + -
63A GLU* 3.6 30.3 - - + -
66A LEU* 3.8 13.0 - - + -
260A LEU* 4.0 14.1 - - + -
299A HIS* 3.0 25.0 + - + +
300A GLY* 3.4 11.0 - - - +
301A ALA 3.2 0.2 - - - -
302A SER* 1.3 76.2 - - - +
304A VAL* 1.3 63.1 + - - +
306A THR* 3.2 3.1 + - - -
307A ILE* 3.0 37.1 + - + +
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Residues in contact with VAL 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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84A PHE* 3.8 20.9 - - + -
87A CYS* 5.4 1.1 - - + -
88A THR* 5.5 0.7 - - - +
254A CYS* 3.9 13.0 - - + -
258A PHE* 3.8 24.5 - - + -
260A LEU* 3.6 21.3 - - + -
265A VAL* 3.9 13.7 - - + -
300A GLY 3.0 18.4 + - - +
301A ALA 3.2 6.3 + - - +
303A VAL* 1.3 75.1 - - - +
305A ALA* 1.3 63.9 + - - +
307A ILE* 3.2 2.3 + - - +
308A LEU* 2.9 46.4 + - + +
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Residues in contact with ALA 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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81A LEU* 3.8 19.5 - - + -
83A GLU* 3.8 27.4 - - + +
84A PHE* 3.9 10.5 - - - +
87A CYS* 4.5 10.0 - - - -
301A ALA 2.9 16.1 + - - +
302A SER 3.9 1.3 - - - +
304A VAL* 1.3 77.5 - - - +
306A THR* 1.3 56.9 + - - +
308A LEU* 4.3 0.2 - - - +
309A SER* 2.7 38.8 + - - -
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Residues in contact with THR 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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62A ALA* 3.9 23.3 - - + +
65A TYR* 3.9 28.3 - - + -
66A LEU* 3.7 17.2 - - - +
83A GLU* 5.0 1.1 + - - -
302A SER 2.6 23.1 + - - -
303A VAL 3.4 4.0 - - - -
305A ALA* 1.3 79.6 - - - +
307A ILE* 1.3 63.9 + - - +
309A SER* 3.5 11.0 + - - -
310A ASN* 3.6 15.9 - - + +
313A LEU* 4.0 10.9 - - + +
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Residues in contact with ILE 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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58A SER* 3.7 40.2 - - - +
59A VAL* 3.9 2.7 - - + +
62A ALA* 3.8 5.8 - - + -
258A PHE* 3.8 32.1 - - + -
303A VAL* 3.0 29.3 + - + +
304A VAL 3.6 5.6 - - - +
306A THR* 1.3 76.1 - - - +
308A LEU* 1.3 60.7 + - - +
310A ASN 3.1 25.5 + - - +
313A LEU* 3.8 19.4 - - + +
314A ARG* 3.3 8.4 + - - -
317A TRP* 3.6 28.3 - - + -
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Residues in contact with LEU 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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87A CYS* 3.6 38.2 - - + +
88A THR* 5.6 0.2 - - - -
91A LEU* 3.8 24.2 - - + -
258A PHE* 4.1 7.9 - - + -
304A VAL* 2.9 34.9 + - + +
307A ILE* 1.3 77.3 - - + +
309A SER* 1.3 59.1 + - - +
310A ASN 3.2 2.9 + - - -
311A ASP* 5.5 1.4 - - - +
314A ARG* 4.0 38.7 + - + +
317A TRP* 3.6 37.2 - - + -
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 3.2 30.5 + - - -
87A CYS* 4.8 5.2 - - - -
305A ALA 2.7 21.2 + - - -
306A THR* 3.5 8.1 + - - -
308A LEU* 1.3 76.8 - - - +
310A ASN* 1.3 59.0 + - - +
311A ASP* 5.5 1.3 - - - -
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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
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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