Contacts of the helix formed by residues 83 - 97 (chain A) in PDB entry 4HVY
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 THR 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A MET* 4.1 2.6 - - - +
81A GLY 5.8 0.2 - - - +
82A GLU* 1.3 76.3 - - - +
84A ILE* 1.3 60.2 + - - +
85A VAL* 3.6 6.6 + - - +
86A GLU* 3.0 40.2 + - - +
87A ALA* 2.9 27.0 + - - +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TYR* 4.7 10.1 - - + -
45A MET 4.3 4.7 - - - +
46A VAL* 3.8 22.6 - - + +
78A MET* 4.0 22.9 - - + -
83A THR* 1.3 75.6 - - - +
85A VAL* 1.3 65.9 + - + +
87A ALA* 3.3 7.4 + - + +
88A LEU* 2.9 25.1 + - - +
118A PHE* 4.1 30.7 - - + -
120A PHE* 3.9 29.1 - - + -
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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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83A THR* 3.3 6.1 + - - +
84A ILE* 1.3 84.5 - - + +
86A GLU* 1.3 60.4 + - - +
88A LEU* 3.1 8.7 + - + +
89A GLN* 2.9 34.3 + - + +
101A GLU* 5.2 1.1 - - - +
102A PRO* 3.8 37.7 - - + -
120A PHE* 4.4 13.5 - - + -
205A NA 3.7 17.5 - - - -
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Residues in contact with GLU 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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81A GLY 4.3 2.4 - - - +
82A GLU* 3.2 22.7 - - + +
83A THR* 3.0 46.3 + - - +
85A VAL* 1.3 77.4 - - - +
87A ALA* 1.3 56.6 + - - +
89A GLN* 3.4 9.4 + - - +
90A ARG* 2.9 29.5 + - - +
205A NA 3.9 12.8 - - - -
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Residues in contact with ALA 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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46A VAL* 3.9 12.6 - - + -
78A MET* 3.7 22.4 - - + -
82A GLU* 3.3 27.1 + - - +
83A THR 2.9 12.3 + - - +
84A ILE* 3.5 10.1 - - + +
85A VAL 3.2 0.2 - - - -
86A GLU* 1.3 72.5 - - - +
88A LEU* 1.3 67.0 + - - +
90A ARG* 3.2 6.0 + - - +
91A VAL* 2.9 28.9 + - - +
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Residues in contact with LEU 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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46A VAL* 3.8 26.4 - - + +
47A LEU 4.1 3.1 - - - +
48A ALA* 3.5 37.0 - - + +
84A ILE 2.9 13.8 + - - +
85A VAL* 3.1 12.1 + - + +
87A ALA* 1.3 76.7 - - - +
89A GLN* 1.3 64.0 + - + +
91A VAL* 3.9 2.0 - - + +
92A VAL* 3.0 30.4 + - + +
100A CYS* 4.5 8.7 - - - -
102A PRO* 3.9 30.7 - - + -
120A PHE* 3.8 28.5 - - + -
122A ALA* 4.7 6.7 - - + -
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Residues in contact with GLN 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* 2.9 25.4 + - + +
86A GLU* 3.8 10.1 - - - +
88A LEU* 1.3 79.2 - - + +
90A ARG* 1.3 56.6 + - - +
92A VAL* 3.4 2.1 + - - +
93A LYS* 2.9 30.9 + - - +
98A LEU 4.7 1.6 - - - +
99A HIS* 6.1 0.2 - - - -
100A CYS* 3.1 41.3 + - - +
101A GLU* 3.5 24.2 + - - +
102A PRO* 5.3 0.7 - - + -
205A NA 2.8 27.6 - - - -
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Residues in contact with ARG 90 (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 GLY* 5.9 0.2 - - - -
77A ARG 2.8 26.9 + - - +
78A MET* 4.1 0.6 - - - +
79A GLU* 3.4 33.5 + - - +
82A GLU* 2.8 36.5 + - - +
86A GLU 2.9 17.2 + - - +
87A ALA* 3.7 7.0 - - - +
89A GLN* 1.3 75.4 - - - +
91A VAL* 1.3 75.5 + - - +
93A LYS* 3.3 7.4 + - + +
94A GLU* 2.9 72.6 + - + +
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Residues in contact with VAL 91 (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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46A VAL* 4.0 11.2 - - + -
48A ALA* 6.3 0.2 - - + -
74A PRO* 3.7 4.9 - - + -
75A ALA* 3.1 42.0 - - - +
76A GLY* 3.7 25.1 - - - +
87A ALA 2.9 19.7 + - - +
88A LEU* 3.9 3.6 - - + +
90A ARG* 1.3 92.1 - - - +
92A VAL* 1.3 58.8 + - + +
94A GLU* 3.9 6.9 - - - +
95A GLU* 2.9 39.4 + - - +
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Residues in contact with VAL 92 (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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48A ALA* 3.7 29.6 - - + -
50A PHE* 3.7 24.5 - - + -
58A LEU* 5.0 0.4 - - + -
74A PRO* 4.1 11.9 - - + -
88A LEU* 3.0 22.7 + - + +
89A GLN 3.9 1.8 - - - +
91A VAL* 1.3 77.7 - - + +
93A LYS* 1.3 56.3 + - - +
96A ALA* 2.8 31.7 + - + -
97A GLY 3.2 4.7 + - - -
98A LEU* 3.5 26.4 + - + +
100A CYS* 3.8 20.4 - - - -
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Residues in contact with LYS 93 (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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89A GLN 2.9 18.1 + - - +
90A ARG* 3.6 7.2 - - + +
92A VAL* 1.3 76.0 - - - +
94A GLU* 1.3 64.6 + - + +
97A GLY* 2.9 33.1 + - - +
98A LEU 3.5 16.3 + - - +
99A HIS* 5.2 11.7 - - + +
130A LYS* 5.3 0.5 - - - +
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Residues in contact with GLU 94 (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 GLU* 4.9 2.1 - - - +
90A ARG* 2.9 61.0 + - + +
91A VAL* 4.0 4.8 - - - +
93A LYS* 1.3 81.6 - - + +
95A GLU* 1.3 62.9 + - + +
130A LYS* 2.9 24.1 + - - +
136A ASP* 4.5 1.7 - - - +
138A GLU* 3.6 36.7 - - + +
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Residues in contact with GLU 95 (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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60A ILE* 3.6 29.6 - - + +
62A GLU* 5.6 1.5 - - - +
73A LEU 4.2 0.2 - - - +
74A PRO* 3.2 10.4 - - + +
75A ALA 2.6 44.0 + - - +
76A GLY* 4.8 0.2 - - - -
91A VAL* 2.9 25.5 + - + +
94A GLU* 1.3 82.1 - - + +
96A ALA* 1.3 59.8 + - - +
130A LYS* 3.5 5.3 - - - +
138A GLU* 3.7 25.8 - - + +
139A SER* 2.7 28.9 + - - +
141A GLN 4.1 0.2 - - - +
142A ALA* 3.8 5.4 - - - +
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Residues in contact with ALA 96 (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 LEU* 3.9 26.0 - - + -
60A ILE* 4.0 7.0 - - + -
74A PRO* 4.8 2.5 - - + -
92A VAL* 2.8 16.6 + - + +
95A GLU* 1.3 80.3 - - - +
97A GLY* 1.3 56.6 + - - +
98A LEU* 3.2 9.4 + - + +
129A LEU* 3.5 9.7 - - - +
130A LYS* 2.9 25.2 + - - -
142A ALA* 3.6 19.3 - - + -
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Residues in contact with GLY 97 (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 VAL 3.2 1.0 + - - -
93A LYS* 2.9 25.5 + - - +
95A GLU 3.9 0.4 - - - -
96A ALA* 1.3 75.2 - - - +
98A LEU* 1.3 60.4 + - - +
99A HIS* 4.6 2.8 - - - -
127A GLY* 3.6 4.2 - - - -
128A ILE 3.2 33.2 + - - +
130A LYS* 4.0 8.3 - - - +
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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