Contacts of the helix formed by residues 77 - 89 (chain A) in PDB entry 4GSA
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A LYS* 5.0 11.7 - - - +
49A ASP* 5.0 5.8 - - - +
75A ALA 3.1 7.3 - - - +
76A HIS* 1.3 98.3 - - + +
78A GLU* 1.3 57.8 + - + +
80A ILE* 3.8 11.1 - - + +
81A GLU* 3.0 38.4 + - - +
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Residues in contact with GLU 78 (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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76A HIS* 3.1 21.7 + - + +
77A PRO* 1.3 79.3 - - + +
79A VAL* 1.3 61.6 + - - +
81A GLU* 3.8 15.5 - - - +
82A ALA* 3.5 20.6 + - - +
318A LYS* 3.7 26.2 - - + +
322A LEU* 4.0 26.5 - - + +
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Residues in contact with VAL 79 (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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72A CYS* 5.7 2.0 - - + -
76A HIS* 3.0 19.3 + - + +
78A GLU* 1.3 75.4 - - - +
80A ILE* 1.3 64.4 + - + +
82A ALA* 3.1 6.8 + - - +
83A LEU* 3.0 42.3 + - + +
277A GLY 4.5 15.7 - - - +
315A ALA* 4.7 11.2 - - - -
318A LYS* 4.0 19.7 - - + -
319A THR* 4.1 15.0 - - - +
322A LEU* 4.0 25.1 - - + -
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Residues in contact with ILE 80 (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 ALA* 4.3 27.1 - - + +
76A HIS 3.0 13.6 + - - +
77A PRO* 3.8 13.2 - - + +
79A VAL* 1.3 77.7 - - + +
81A GLU* 1.3 68.1 + - + +
83A LEU* 3.4 9.1 + - + +
84A LYS* 3.1 36.9 + - - +
87B MET* 4.0 39.1 - - + +
88B GLU* 4.4 13.9 - - + +
91B THR* 5.0 9.9 - - + -
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Residues in contact with GLU 81 (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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77A PRO* 3.0 26.1 + - - +
78A GLU* 3.8 18.6 - - - +
80A ILE* 1.3 79.0 - - + +
82A ALA* 1.3 66.1 + - - +
84A LYS* 3.1 24.1 + - + +
85A VAL* 3.1 19.5 + - + +
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Residues in contact with ALA 82 (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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78A GLU 3.5 12.3 + - - +
79A VAL 3.1 10.5 + - - +
81A GLU* 1.3 84.5 - - + +
83A LEU* 1.3 56.5 + - - +
85A VAL* 3.7 6.9 + - - +
86A ALA* 3.2 26.5 + - - +
314A THR* 3.7 19.7 - - + +
318A LYS* 4.3 22.9 - - + +
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Residues in contact with LEU 83 (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 VAL* 3.0 30.6 + - + +
80A ILE* 3.8 11.0 - - + +
82A ALA* 1.3 76.1 - - - +
84A LYS* 1.3 57.5 + - - +
86A ALA* 3.8 2.8 - - - +
87A MET* 3.0 36.9 + - + +
279A LEU* 4.1 26.7 - - + -
311A LEU* 3.6 35.0 - - + +
314A THR* 4.2 6.3 - - + -
315A ALA* 3.9 16.8 - - + +
87B MET* 3.7 28.9 - - + -
91B THR* 4.6 5.8 - - + -
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Residues in contact with LYS 84 (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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80A ILE* 3.1 28.1 + - - +
81A GLU* 3.1 17.4 + - + +
83A LEU* 1.3 74.3 - - - +
85A VAL* 1.3 66.9 + - + +
87A MET* 3.4 21.3 - - - +
88A GLU* 3.8 15.1 + - - +
84B LYS* 3.2 49.3 + - + +
87B MET* 4.3 13.8 - - - +
88B GLU* 4.5 14.5 + - - +
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Residues in contact with VAL 85 (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 GLU* 3.1 14.8 + - + +
82A ALA* 4.0 6.3 - - - +
84A LYS* 1.3 77.1 - - + +
86A ALA* 1.3 64.2 + - - +
88A GLU* 3.2 24.8 - - - +
89A LYS* 4.2 11.2 + - + +
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Residues in contact with ALA 86 (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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82A ALA 3.2 16.7 + - - +
83A LEU* 3.8 6.1 - - - +
84A LYS 3.3 0.2 - - - -
85A VAL* 1.3 76.7 - - - +
87A MET* 1.3 58.4 + - - +
88A GLU 2.9 4.3 - - - -
89A LYS* 2.8 37.1 + - - +
90A GLY 3.9 4.7 + - - +
99A LEU* 5.9 1.1 - - + -
310A PRO* 5.1 4.2 - - + +
311A LEU* 4.0 12.6 - - + -
314A THR* 3.8 22.7 - - + +
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Residues in contact with MET 87 (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 LEU* 3.0 18.4 + - + +
84A LYS* 3.4 13.5 - - - +
86A ALA* 1.3 77.4 - - - +
88A GLU* 1.3 62.1 + - - +
89A LYS 3.1 0.4 - - - -
90A GLY* 3.2 18.4 + - - -
91A THR* 4.3 10.0 + - + +
311A LEU* 3.7 29.1 - - + +
75B ALA* 4.7 0.3 - - - +
80B ILE* 3.8 33.0 - - + +
83B LEU* 4.1 21.5 - - + -
84B LYS* 3.6 29.6 - - + -
87B MET* 4.1 27.1 - - + -
311B LEU* 5.3 1.1 - - + -
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Residues in contact with GLU 88 (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 LYS 4.0 10.9 - - - +
85A VAL* 3.2 21.5 + - - +
86A ALA 2.8 0.8 + - - -
87A MET* 1.3 83.2 - - - +
89A LYS* 1.3 61.6 + - + +
90A GLY 3.6 0.5 + - - -
47B VAL 5.0 0.9 - - - +
48B LYS* 5.1 6.8 - - - +
75B ALA* 4.3 10.6 - - - +
80B ILE* 3.7 23.5 - - + +
84B LYS* 3.9 22.2 - - - +
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Residues in contact with LYS 89 (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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85A VAL* 4.4 13.7 - - + +
86A ALA* 2.8 18.6 + - - +
88A GLU* 1.3 81.0 - - + +
90A GLY* 1.3 56.5 + - - +
93A PHE* 3.7 5.5 - - + -
45B ASP* 3.7 34.4 + - - +
46B ARG* 3.3 28.3 - - + -
47B VAL* 2.9 32.1 + - - +
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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