Contacts of the helix formed by residues 85 - 100 (chain A) in PDB entry 2CRX
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 LEU 4.0 0.2 + - - -
84A ALA* 1.3 72.5 - - - +
86A LYS* 1.3 56.5 + - - +
87A THR 3.0 0.2 + - - -
88A ILE* 3.2 7.9 + - - +
89A GLN* 2.8 51.8 + - - +
117A MET* 3.8 13.5 - - + -
120A ILE* 4.9 2.7 - - + +
121A ARG* 3.7 34.1 - - + +
124A ASN* 3.9 21.5 - - + +
125A VAL* 5.4 3.4 - - + +
129A GLU* 2.7 32.9 + - + +
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA* 3.3 3.0 - - + +
85A VAL* 1.3 78.0 - - - +
87A THR* 1.3 57.3 + - - +
89A GLN* 4.0 10.7 - - + +
90A GLN* 3.4 20.6 + - - +
13D T 4.1 20.3 - - + +
14D A 3.4 41.2 + - + +
15D G 2.7 38.4 + - - -
16D C 4.5 6.9 - - - +
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Residues in contact with THR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.8 23.3 - - + -
84A ALA 3.0 10.2 + - - -
85A VAL 3.0 0.2 - - - -
86A LYS* 1.3 76.3 - - - +
88A ILE* 1.3 61.9 + - - +
89A GLN 3.1 1.6 - - - -
90A GLN* 2.9 27.9 + - - +
91A HIS* 3.0 16.2 + - + -
12D A 3.3 24.7 - - + +
13D T 2.8 49.4 + - + +
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.4 33.8 - - + +
78A LEU* 3.9 24.9 - - + -
79A GLN* 3.9 24.2 - - + +
83A LEU* 3.7 25.4 - - + +
84A ALA 3.0 17.2 + - - +
85A VAL* 3.8 4.9 - - - +
87A THR* 1.3 74.8 - - - +
89A GLN* 1.3 57.2 + - - +
91A HIS* 3.3 2.9 + - - +
92A LEU* 2.9 25.1 + - - +
117A MET* 4.1 16.2 - - + -
120A ILE* 3.9 21.3 - - + -
124A ASN* 4.9 2.0 - - - +
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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
----------------------------------------------------------
85A VAL* 2.8 36.5 + - - +
86A LYS* 4.1 10.1 - - + +
88A ILE* 1.3 74.8 - - - +
90A GLN* 1.3 58.1 + - - +
92A LEU* 4.3 8.1 - - + +
93A GLY* 2.7 31.0 + - - -
117A MET* 3.3 35.2 - - + +
121A ARG* 5.0 4.8 - - - +
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Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 3.3 29.7 - - + +
48A VAL* 3.2 24.2 - - - +
86A LYS 3.4 13.5 + - - +
87A THR 2.9 14.7 + - - +
89A GLN* 1.3 78.7 - - - +
91A HIS* 1.3 66.8 + - + +
93A GLY* 3.1 2.7 + - - -
94A GLN* 2.9 55.1 + - - +
12D A 5.6 0.2 - - - +
13D T 3.6 26.3 - - + +
14D A 5.3 4.8 + - - +
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Residues in contact with HIS 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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48A VAL* 3.8 27.5 - - + +
51A SER* 3.3 16.6 + - - -
74A TYR* 2.8 34.7 + - + -
75A LEU* 4.9 1.3 - - + -
78A LEU* 3.3 28.7 - - + +
81A ARG* 4.7 1.1 - - - -
83A LEU* 4.7 0.2 - - - +
87A THR* 3.0 29.0 + - + +
88A ILE 3.4 8.1 - - - +
90A GLN* 1.3 90.8 - - + +
92A LEU* 1.3 65.1 + - - +
93A GLY 3.1 0.3 + - - -
94A GLN 3.3 0.2 + - - -
95A LEU* 3.1 27.8 + - - +
11D T 6.1 0.7 - - - -
12D A 3.5 28.4 + - - -
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Residues in contact with LEU 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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71A VAL* 4.3 9.9 - - + -
75A LEU* 3.7 23.0 - - + +
88A ILE 2.9 18.7 + - - +
89A GLN* 4.0 10.1 - - + +
91A HIS* 1.3 72.9 - - - +
93A GLY* 1.3 57.3 + - - +
95A LEU* 3.5 4.8 + - + +
96A ASN* 3.0 40.8 + - - +
107A PRO* 4.1 12.3 - - + -
108A SER* 3.1 23.1 - - - +
113A VAL* 3.9 21.8 - - + -
117A MET* 3.9 24.9 - - + -
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Residues in contact with GLY 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 2.7 23.1 + - - -
90A GLN* 3.4 1.6 - - - -
91A HIS 3.1 0.2 - - - -
92A LEU* 1.3 71.3 - - - +
94A GLN* 1.3 60.5 + - - +
96A ASN* 3.0 12.5 + - - +
97A MET* 2.9 26.3 + - - +
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Residues in contact with GLN 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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41A THR* 3.7 14.1 + - - +
44A MET* 3.6 6.4 - - - +
45A LEU* 3.4 42.9 + - + +
48A VAL* 3.5 20.0 - - + -
90A GLN* 2.9 49.4 + - - +
93A GLY* 1.3 72.7 - - - +
95A LEU* 1.3 61.9 + - - +
97A MET* 2.9 27.0 + - - +
98A LEU* 2.8 23.0 - - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 3.8 19.5 - - + +
49A CYS* 5.2 4.7 - - - -
52A TRP* 4.1 33.7 - - + +
66A ALA* 5.2 0.2 - - + -
71A VAL* 4.4 18.6 - - + -
74A TYR* 4.1 30.5 - - + -
75A LEU* 6.0 0.2 - - + -
91A HIS 3.1 20.9 + - - +
92A LEU* 3.6 6.5 - - - +
94A GLN* 1.3 77.8 - - - +
96A ASN* 1.3 60.8 + - - +
98A LEU* 4.0 11.0 + - + +
99A HIS* 2.8 39.0 + - + +
107A PRO* 4.3 13.7 - - + -
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Residues in contact with ASN 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 LEU* 3.0 29.8 + - - +
93A GLY* 3.0 12.4 + - - +
95A LEU* 1.3 76.5 - - - +
97A MET* 1.3 65.6 + - - +
99A HIS 3.7 0.2 + - - -
100A ARG* 3.3 21.3 + - - +
106A ARG* 3.4 25.0 + - + +
107A PRO* 3.1 16.2 - - - +
108A SER* 2.6 52.1 + - - -
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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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30A MET* 4.5 13.7 - - + -
37A PHE* 3.8 39.0 - - + -
41A THR* 6.6 0.2 - - - -
42A TRP* 5.3 2.7 - - + -
45A LEU* 4.3 24.7 - - + -
93A GLY 2.9 11.2 + - - +
94A GLN* 2.9 24.5 + - - +
96A ASN* 1.3 75.5 - - - +
98A LEU* 1.3 61.8 + - - +
100A ARG* 2.9 9.5 + - - +
101A ARG* 2.9 52.1 + - + +
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Residues in contact with LEU 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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27A LEU* 5.6 4.7 - - + -
30A MET* 4.8 11.4 - - + -
45A LEU* 3.3 30.5 - - + -
49A CYS* 4.3 16.8 - - - -
63A TRP* 5.0 13.5 - - + -
64A PHE* 4.7 17.5 - - + -
94A GLN 2.8 31.6 - - - +
95A LEU* 4.1 11.4 - - + +
97A MET* 1.3 80.6 - - + +
99A HIS* 1.3 70.2 + - + +
101A ARG* 3.1 14.7 + - - -
102A SER* 2.6 30.7 + - - +
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Residues in contact with HIS 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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52A TRP* 5.7 0.9 - - - -
63A TRP 4.8 1.3 - - - -
64A PHE* 3.8 19.6 - + - -
65A PRO* 3.7 7.2 - - + +
66A ALA* 2.8 49.5 + - + +
95A LEU* 2.8 31.3 + - + +
96A ASN 4.0 1.1 - - - +
97A MET 3.3 1.2 - - - -
98A LEU* 1.3 84.9 - - + +
100A ARG* 1.3 50.2 + - - +
102A SER 2.4 24.1 - - - +
104A LEU* 2.4 39.0 + - + +
105A PRO* 3.6 24.5 - - + +
106A ARG* 4.0 9.0 - - - -
107A PRO* 4.0 9.0 - - + -
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Residues in contact with ARG 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 ASN 3.3 11.1 + - - +
97A MET* 2.9 10.8 + - - +
99A HIS* 1.3 75.2 - - - +
101A ARG* 1.3 63.5 + - + +
102A SER 2.9 16.4 + - - +
103A GLY* 5.1 0.3 - - - -
104A LEU 4.1 4.5 - - - -
106A ARG* 3.1 46.0 - - + +
109A ASP* 4.3 5.7 + - - -
111B ASN* 5.0 1.7 + - - +
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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