Contacts of the helix formed by residues 86 - 105 (chain A) in PDB entry 2HC5
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TYR* 4.9 1.1 - - - +
68A GLU* 6.4 1.3 - - + -
70A TYR* 3.5 8.5 - - + -
84A GLU 3.6 8.3 - - - +
85A ILE* 1.3 90.3 - - + +
87A PRO* 1.3 71.2 - - + +
88A LYS* 3.1 12.6 - - + -
89A ARG* 2.8 60.7 + - + +
90A TRP* 3.0 8.7 + - - +
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Residues in contact with PRO 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 3.4 42.6 - - + +
40A LEU* 4.3 7.6 - - + -
68A GLU* 4.1 22.9 - - + +
69A TYR* 3.4 40.6 - - + +
70A TYR* 3.7 9.0 - - + -
71A VAL* 5.9 0.4 - - + +
85A ILE 3.8 0.8 - - - +
86A PRO* 1.3 86.7 - - + +
88A LYS* 1.3 59.1 + - + +
89A ARG 3.1 4.0 + - - -
90A TRP* 3.3 20.8 + - + +
91A LEU* 4.3 1.7 + - - +
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Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 5.0 4.3 - - - -
68A GLU* 5.2 10.1 - - - +
86A PRO* 4.2 16.2 - - + -
87A PRO* 1.3 81.7 - - + +
89A ARG* 1.3 69.5 + - + +
91A LEU* 5.2 5.1 - - - +
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Residues in contact with ARG 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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16A TYR* 3.8 19.0 + - - +
20A ILE* 3.4 46.0 - - + +
23A GLN* 6.5 0.7 - - - -
85A ILE* 3.8 2.6 - - + +
86A PRO* 2.8 34.0 + - + +
88A LYS* 1.3 89.2 - - + +
90A TRP* 1.3 65.0 + - - +
91A LEU* 3.2 3.4 - - - -
92A ASP* 3.2 18.1 + - - +
93A PHE* 3.2 12.8 + - - +
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Residues in contact with TRP 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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35A VAL* 5.5 2.2 - - + -
40A LEU* 4.5 16.3 + - + -
43A MET* 3.4 37.6 - - + +
44A VAL* 3.8 30.2 - - + +
47A MET* 4.5 12.6 - - + -
60A PHE* 3.7 18.2 - + - -
71A VAL* 3.7 35.0 - - + -
85A ILE* 3.7 34.1 - - + +
86A PRO 3.0 8.9 + - - +
87A PRO* 3.3 20.3 + - + +
89A ARG* 1.3 79.0 - - - +
91A LEU* 1.3 56.2 + - + +
93A PHE* 3.5 27.9 - + - +
94A TYR* 2.8 39.8 + - + +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 5.3 2.6 - - + +
31A PRO* 3.4 35.2 - - + +
32A VAL* 4.3 3.1 - - + -
33A HIS* 3.5 39.5 - - + +
35A VAL* 4.0 22.2 - - + -
43A MET* 4.4 22.0 - - + -
87A PRO 4.7 0.9 - - - +
88A LYS* 5.8 3.8 - - - +
89A ARG* 3.2 1.5 - - - -
90A TRP* 1.3 80.9 - - + +
92A ASP* 1.3 61.5 + - - +
94A TYR* 3.4 12.3 - - + +
95A ALA* 3.2 21.7 + - - +
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Residues in contact with ASP 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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15A ARG* 4.7 5.5 + - - -
16A TYR* 3.6 17.0 - - - -
19A GLN* 2.8 51.1 + - - +
20A ILE* 4.2 12.3 - - + +
30A VAL* 5.5 9.3 - - + +
89A ARG* 3.2 12.5 + - - +
91A LEU* 1.3 76.5 - - - +
93A PHE* 1.3 54.9 + - - +
95A ALA* 3.2 6.8 + - - +
96A ALA* 2.7 39.1 + - - +
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Residues in contact with PHE 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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9A LEU* 5.2 2.2 - - + -
12A VAL* 4.3 14.4 - - + -
13A TRP* 3.6 37.9 - + - -
16A TYR* 3.5 28.4 - + + -
47A MET* 4.4 1.6 - - - -
58A LEU* 5.6 0.9 - - + -
60A PHE* 4.1 11.7 - + - -
73A VAL* 4.8 1.8 - - + -
85A ILE* 4.3 18.6 - - + -
89A ARG 3.2 7.5 + - - +
90A TRP* 3.5 42.0 - + - +
92A ASP* 1.3 78.5 + - - +
94A TYR* 1.3 67.3 + - - +
96A ALA* 3.5 2.1 - - - +
97A MET* 3.0 57.4 + - + +
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Residues in contact with TYR 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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31A PRO* 4.3 24.7 - - + -
43A MET* 3.8 29.2 - - + -
46A GLU* 2.6 34.8 + - + -
47A MET* 4.2 21.6 - - + +
50A LEU* 6.2 0.4 - - + -
90A TRP* 2.8 27.3 + - + +
91A LEU* 3.4 12.8 - - + +
93A PHE* 1.3 78.8 - - - +
95A ALA* 1.3 55.9 + - - +
97A MET* 3.9 1.2 - - - +
98A THR* 2.6 52.8 + - + -
112A HIS* 3.2 13.4 + + - -
114A HIS* 3.0 28.5 + + + -
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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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15A ARG* 3.7 12.6 - - - +
30A VAL* 5.1 5.6 - - + -
31A PRO* 4.3 22.0 - - + -
91A LEU 3.2 11.5 + - - +
92A ASP* 3.2 8.3 + - - +
94A TYR* 1.3 79.7 - - - +
96A ALA* 1.3 67.0 + - - +
98A THR* 3.1 5.5 + - - -
99A GLU* 2.9 39.9 + - - +
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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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12A VAL* 4.4 18.1 - - + +
15A ARG* 3.3 43.9 + - + +
16A TYR* 4.7 7.2 - - + -
92A ASP* 2.7 26.6 + - - +
93A PHE* 3.5 9.9 - - - +
95A ALA* 1.3 74.5 - - - +
97A MET* 1.3 59.7 + - - +
99A GLU* 4.0 0.2 - - - +
100A PHE* 3.5 17.0 + - - +
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Residues in contact with MET 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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9A LEU* 3.6 31.2 - - - -
12A VAL* 4.0 21.1 - - + -
47A MET* 3.4 40.8 - - + -
51A LEU* 3.8 23.3 - - + -
60A PHE* 4.0 2.5 - - + -
93A PHE* 3.0 35.9 + - + +
94A TYR 4.4 1.3 - - - +
96A ALA* 1.3 75.4 - - - +
98A THR* 1.3 55.6 + - - +
100A PHE* 3.2 4.5 + - - +
101A LEU* 2.6 52.7 + - + +
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Residues in contact with THR 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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47A MET* 4.1 9.0 - - - +
50A LEU* 5.3 3.6 - - + +
94A TYR* 2.6 47.6 + - + -
95A ALA* 3.6 6.7 - - - -
97A MET* 1.3 73.8 - - - +
99A GLU* 1.3 65.8 + - - +
101A LEU* 4.4 3.8 - - - +
102A GLY* 2.7 34.8 + - - +
110A LEU* 6.5 0.2 - - + -
112A HIS* 3.5 30.4 - - + +
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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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15A ARG* 2.8 46.8 + - - +
95A ALA* 2.9 26.1 + - - +
96A ALA 4.0 0.7 - - - +
98A THR* 1.3 85.7 - - - +
100A PHE* 1.3 59.5 + - - +
102A GLY* 4.1 0.7 - - - -
103A LEU* 2.9 34.7 + - + +
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Residues in contact with PHE 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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6A LEU* 3.5 35.9 - - + -
8A THR* 3.9 15.0 - - + -
9A LEU* 4.8 1.8 - - + -
11A PRO* 3.5 41.3 - - + -
12A VAL* 3.4 24.9 - - + -
96A ALA 3.5 11.7 + - - +
97A MET* 3.2 7.2 + - + +
98A THR 3.2 0.4 - - - -
99A GLU* 1.3 79.3 - - - +
101A LEU* 1.3 75.5 + - + +
103A LEU* 3.2 19.6 + - + +
104A PHE* 3.1 41.6 - + - -
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Residues in contact with LEU 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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3A ILE* 4.0 11.9 - - + -
6A LEU* 3.8 16.8 - - + -
47A MET* 4.4 8.1 - - + -
50A LEU* 3.9 26.5 - - + +
51A LEU* 3.6 39.0 - - + -
97A MET* 2.6 45.4 + - + +
98A THR* 4.3 3.1 - - - +
100A PHE* 1.3 90.1 - - + +
102A GLY* 1.3 58.2 + - - +
104A PHE* 2.8 21.8 + - - +
105A VAL* 2.9 19.3 + - + +
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Residues in contact with GLY 102 (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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98A THR* 2.7 24.6 + - - +
99A GLU* 4.1 1.6 - - - -
101A LEU* 1.3 72.2 - - - +
103A LEU* 1.3 59.8 + - - +
104A PHE 3.2 0.2 - - - -
105A VAL* 3.2 32.0 - - - +
107A GLU* 4.4 17.4 - - - +
110A LEU* 5.4 7.4 - - - -
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Residues in contact with LEU 103 (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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1A LEU* 3.7 29.5 + - + +
99A GLU* 2.9 24.4 + - + +
100A PHE* 3.2 17.0 + - + +
101A LEU 3.0 0.8 - - - -
102A GLY* 1.3 81.1 - - - +
104A PHE* 1.3 63.3 + - + +
105A VAL 4.5 1.0 - - - +
107A GLU* 5.8 3.8 - - - +
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Residues in contact with PHE 104 (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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1A LEU* 3.1 53.3 + - + +
2A ASN 3.3 26.0 - - - -
3A ILE* 3.6 27.3 + - + +
6A LEU* 3.9 27.1 - - + -
100A PHE* 3.1 57.7 - + - -
101A LEU* 2.8 10.0 + - - +
103A LEU* 1.3 80.6 - - + +
105A VAL* 1.3 64.7 + - - +
106A ASP 3.9 0.5 + - - -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.3 25.6 - - + -
50A LEU* 4.5 28.5 - - + +
53A PRO* 6.0 2.9 - - + -
101A LEU* 2.9 20.2 + - + +
102A GLY* 3.2 30.5 - - - +
103A LEU 4.4 1.6 - - - +
104A PHE* 1.3 81.4 - - - +
106A ASP* 1.3 66.1 + - - +
107A GLU* 3.0 9.4 + - - +
109A LYS* 6.4 0.2 - - + -
110A LEU* 5.0 12.6 - - + -
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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