Contacts of the helix formed by residues 85 - 101 (chain A) in PDB entry 3HVH
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 VAL 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A MET 3.9 0.6 + - - -
84A ASN* 1.3 71.8 - - - +
86A GLY* 1.3 64.0 + - - +
88A ALA 5.1 0.2 + - - -
89A LYS* 3.5 47.2 + - + +
90A GLY* 4.0 3.8 - - - +
93A MET* 3.6 32.1 - - + -
114A TYR* 3.4 24.6 - - + +
115A SER* 4.1 14.0 - - - -
118A ARG* 5.0 0.9 - - - -
182A PHE* 4.7 6.3 - - + -
184A ASP* 4.9 6.4 + - - +
212A ASP* 4.3 18.6 - - - +
242A GLU* 3.5 10.3 - - - +
250A LEU* 5.0 1.1 - - + -
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Residues in contact with GLY 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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73A ASP* 3.9 8.5 - - - -
84A ASN 3.1 3.0 + - - -
85A VAL* 1.3 81.4 - - - +
87A ASP* 1.3 61.2 + - - -
88A ALA 3.4 2.2 - - - -
90A GLY* 2.8 27.4 + - - -
114A TYR* 3.3 19.4 + - - -
242A GLU* 4.0 10.1 - - - -
243A TYR* 4.0 8.1 - - - -
268A CL 4.1 4.5 - - - -
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Residues in contact with ASP 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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66A GLN* 5.8 2.4 + - - -
73A ASP* 3.8 18.7 + - + +
86A GLY* 1.3 72.4 - - - -
88A ALA* 1.3 60.1 + - - +
91A GLN* 2.9 54.8 + - - +
114A TYR* 3.4 5.6 + - - -
118A ARG* 3.0 29.1 + - - +
243A TYR* 6.1 0.2 - - + -
268A CL 3.5 9.8 - - + +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLY 3.4 0.8 - - - -
87A ASP* 1.3 79.5 - - - +
89A LYS* 1.3 62.6 + - - +
91A GLN* 3.4 14.4 + - - +
92A ILE* 3.6 12.5 + - - +
239A SER* 3.6 17.4 + - - +
240A TYR* 4.4 22.0 - - + +
268A CL 3.6 15.5 - - + +
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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* 3.5 26.0 + - + +
86A GLY 4.0 1.0 + - - -
88A ALA* 1.3 79.5 - - - +
90A GLY* 1.4 62.8 + - - +
92A ILE* 3.1 9.8 + - - +
93A MET* 3.0 23.6 + - - +
212A ASP* 2.7 30.5 + - - +
213A ASN* 3.3 5.7 - - - +
239A SER* 3.4 23.6 - - - +
240A TYR 3.4 19.7 - - - +
241A LEU* 4.5 0.2 - - - +
242A GLU* 2.9 27.8 + - - +
248A ASP* 2.8 30.8 + - + +
249A GLY 4.7 2.7 - - - +
250A LEU* 3.8 18.4 - - + +
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Residues in contact with GLY 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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85A VAL* 4.0 1.3 - - - +
86A GLY 2.8 22.8 + - - -
87A ASP 3.7 0.9 - - - -
88A ALA 3.2 0.2 - - - -
89A LYS* 1.4 77.4 - - - +
91A GLN* 1.3 55.8 + - - +
93A MET* 3.3 13.0 + - - +
94A ASP* 2.9 33.6 + - - +
118A ARG* 3.3 22.6 + - - -
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Residues in contact with GLN 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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87A ASP* 2.9 40.7 + - - +
88A ALA* 3.7 8.8 - - - +
89A LYS 3.2 0.2 - - - -
90A GLY* 1.3 77.6 - - - +
92A ILE* 1.3 61.4 + - + +
94A ASP* 3.4 7.7 + - - +
95A ALA* 3.1 22.0 + - - +
118A ARG* 3.9 14.4 - - - +
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Residues in contact with ILE 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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88A ALA 3.6 8.5 + - - +
89A LYS* 3.1 8.4 + - - +
91A GLN* 1.3 74.6 - - + +
93A MET* 1.3 67.5 + - - +
95A ALA* 3.1 8.3 + - + +
96A VAL* 3.0 28.8 + - + +
237A TYR* 3.8 39.3 - - + +
238A SER 4.1 9.2 - - - +
239A SER* 3.5 35.4 - - - +
250A LEU* 3.8 17.3 - - + -
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Residues in contact with MET 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 3.6 35.0 - - - -
89A LYS 3.0 15.3 + - - +
90A GLY* 3.5 8.7 - - - +
92A ILE* 1.3 77.8 - - - +
94A ASP* 1.3 65.7 + - - +
96A VAL* 3.2 2.5 + - - +
97A ILE* 2.9 31.4 + - + +
115A SER* 4.0 9.6 - - - +
118A ARG* 5.3 5.6 - - + -
119A MET* 3.8 31.9 - - + -
182A PHE* 3.6 34.1 - - + -
210A LEU* 4.0 19.4 - - + +
250A LEU* 3.9 13.7 - - + -
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Residues in contact with ASP 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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90A GLY 2.9 16.8 + - - +
91A GLN* 3.6 9.8 - - - +
92A ILE 3.2 0.2 - - - -
93A MET* 1.3 75.3 - - - +
95A ALA* 1.3 58.2 + - - +
97A ILE* 3.4 2.0 + - - +
98A ARG* 3.0 49.7 + - - +
118A ARG* 2.9 37.4 + - - +
121A ARG* 2.9 36.3 + - - -
122A LEU* 3.5 16.9 - - + +
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Residues in contact with ALA 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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91A GLN 3.1 10.1 + - - +
92A ILE* 3.1 12.4 + - + +
94A ASP* 1.3 79.5 - - - +
96A VAL* 1.3 62.9 + - + +
98A ARG* 3.6 7.6 + - - +
99A GLU* 3.1 24.2 + - - +
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Residues in contact with VAL 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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92A ILE* 3.0 29.3 + - + +
93A MET 3.7 6.3 - - - +
95A ALA* 1.3 75.7 - - + +
97A ILE* 1.3 65.3 + - - +
99A GLU* 3.2 10.1 + - - +
100A TYR* 3.1 43.7 + - + +
180A MET* 4.1 13.9 - - + -
208A VAL* 4.5 4.0 - - + -
210A LEU* 4.4 28.0 - - + -
237A TYR* 4.8 17.9 - - + +
252A LYS* 4.5 10.1 - - + -
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Residues in contact with ILE 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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93A MET* 2.9 22.3 + - + +
94A ASP* 3.8 4.5 - - - +
96A VAL* 1.3 75.8 - - + +
98A ARG* 1.3 59.6 + - - +
101A SER* 2.9 28.6 + - - -
102A PRO* 3.5 21.4 - - + +
105A VAL* 4.5 6.5 - - + -
119A MET* 4.2 38.1 - - + +
122A LEU* 3.6 40.2 - - + +
123A LEU* 4.6 5.4 - - + -
180A MET* 3.7 27.1 - - - -
210A LEU* 6.2 1.6 - - + -
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Residues in contact with ARG 98 (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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94A ASP* 3.0 44.7 + - - +
95A ALA* 3.9 7.4 - - - +
97A ILE* 1.3 79.3 - - + +
99A GLU* 1.3 63.7 + - - +
101A SER* 3.9 8.9 + - - +
121A ARG* 4.9 4.6 - - - +
122A LEU* 3.4 37.2 - - + +
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Residues in contact with GLU 99 (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 ALA 3.1 18.8 + - - +
96A VAL* 3.2 10.2 + - - +
98A ARG* 1.3 78.9 - - - +
100A TYR* 1.3 90.0 + - + +
101A SER* 5.0 1.0 - - - -
237A TYR* 5.5 0.9 + - - -
252A LYS* 4.5 7.7 + - - -
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Residues in contact with TYR 100 (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 VAL* 3.1 34.0 + - + +
99A GLU* 1.3 105.6 + - + +
101A SER* 1.3 72.2 + - - +
102A PRO* 3.3 3.5 - - + +
180A MET* 3.8 16.4 - - + -
206A GLY 5.6 0.9 - - - -
208A VAL* 3.7 28.5 - - + -
252A LYS* 2.9 38.1 + - + -
254A ILE* 3.4 15.9 - - + +
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Residues in contact with SER 101 (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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97A ILE* 2.9 14.0 + - - -
98A ARG* 4.6 7.4 - - - +
99A GLU 3.6 1.9 - - - -
100A TYR* 1.3 79.2 - - - +
102A PRO* 1.3 59.1 - - - +
124A GLN* 3.6 26.9 + - - +
266A CL 2.7 35.4 - - - +
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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