Contacts of the helix formed by residues 98 - 115 (chain A) in PDB entry 2CHR
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 ALA 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A GLU* 3.4 6.0 + - - +
96A GLY* 3.3 4.4 - - - -
97A ASN* 1.3 74.5 - - - +
99A SER* 1.3 60.4 + - - +
101A LYS* 4.1 9.2 - - + -
102A ALA* 2.8 31.9 + - - +
249A SER 5.8 0.2 - - - +
271A CYS 3.4 12.8 - - - +
272A ASN 4.3 7.6 - - - +
273A MET 4.3 3.1 - - - -
274A GLY* 3.6 21.9 - - - +
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Residues in contact with SER 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY* 3.9 4.1 - - - -
48A GLY 3.0 39.6 + - - -
49A SER* 5.8 0.4 - - - -
56A SER* 6.1 0.2 - - - -
58A GLU* 3.1 23.0 + - - -
63A ILE* 3.4 12.3 - - - -
98A ALA* 1.3 76.6 - - - +
100A ALA* 1.3 58.9 + - - +
102A ALA* 3.3 1.9 + - - +
103A ALA* 2.9 29.5 + - - +
271A CYS* 3.3 24.2 + - - +
298A MET* 5.2 2.7 - - - -
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 3.3 7.7 + - - +
63A ILE* 3.9 21.0 - - + +
66A ILE* 4.0 23.3 - - + -
67A VAL* 3.8 20.1 - - + +
71A LEU* 4.0 4.2 - - + +
97A ASN* 3.6 8.7 - - + +
98A ALA 3.3 0.2 - - - -
99A SER* 1.3 79.9 - - - +
101A LYS* 1.3 62.3 + - - +
103A ALA* 3.4 3.8 + - - +
104A VAL* 3.4 27.5 + - - +
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Residues in contact with LYS 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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71A LEU* 4.2 16.8 - - + -
87A LEU* 4.7 3.5 - - + +
90A MET* 3.6 34.3 + - + +
91A ALA* 4.3 10.2 - - - +
94A VAL* 3.0 36.9 + - + -
95A THR* 4.2 0.4 - - - +
96A GLY* 3.1 32.1 + - - +
97A ASN 3.0 20.2 + - - +
98A ALA* 3.7 9.4 - - + +
99A SER 3.3 0.2 - - - -
100A ALA* 1.3 77.8 - - - +
102A ALA* 1.3 55.3 + - - +
104A VAL 3.7 0.3 + - - -
105A GLU* 3.2 25.5 + - - +
274A GLY* 4.7 9.4 - - - +
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Residues in contact with ALA 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 ALA 2.8 19.7 + - - +
99A SER 3.8 3.6 - - - +
100A ALA 3.3 0.2 - - - -
101A LYS* 1.3 75.1 - - - +
103A ALA* 1.3 67.1 + - - +
105A GLU* 3.3 3.3 + - - +
106A MET* 3.1 35.8 + - + +
270A LEU 3.6 10.1 - - - +
271A CYS* 4.2 8.1 - - - -
274A GLY 4.0 0.8 - - - -
275A GLY* 3.2 34.3 - - - +
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Residues in contact with ALA 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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32A VAL 4.7 0.4 - - - +
34A VAL* 3.7 22.3 - - + +
45A GLY* 4.0 7.4 - - - -
46A GLU 3.5 30.9 + - - +
47A GLY* 3.7 4.9 - - - +
63A ILE* 5.1 2.0 - - + -
67A VAL* 5.0 2.0 - - + -
99A SER 2.9 16.8 + - - +
100A ALA* 3.5 10.3 - - - +
101A LYS 3.4 0.2 - - - -
102A ALA* 1.3 79.1 - - - +
104A VAL* 1.3 62.7 + - - +
106A MET* 3.4 10.7 + - - +
107A ALA* 3.5 10.4 + - - +
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Residues in contact with VAL 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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6A ILE* 4.5 13.9 - - + -
34A VAL* 4.5 13.5 - - + -
36A VAL* 6.3 0.9 - - + -
67A VAL* 4.1 25.4 - - + -
71A LEU* 4.5 13.7 - - + -
72A ALA* 6.0 0.4 - - - +
75A LEU* 3.5 28.3 - - + -
90A MET* 3.9 17.0 - - + -
100A ALA 3.4 14.3 + - - +
101A LYS 4.0 0.9 - - - +
102A ALA 3.3 0.2 - - - -
103A ALA* 1.3 73.5 - - - +
105A GLU* 1.3 64.6 + - - +
107A ALA* 3.3 12.6 + - + +
108A LEU* 3.3 21.5 + - + +
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Residues in contact with GLU 105 (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 VAL* 3.3 22.5 - - - +
87A LEU* 3.8 17.7 - - + +
90A MET* 4.3 6.3 - - - +
101A LYS 3.2 16.8 + - - +
102A ALA* 3.3 8.0 + - - +
104A VAL* 1.3 78.5 - - - +
106A MET* 1.3 66.4 + - + +
108A LEU* 3.3 7.3 + - - +
109A LEU* 3.0 32.6 + - + +
274A GLY 3.4 6.6 - - - +
275A GLY* 3.3 8.4 - - - -
276A VAL* 3.1 30.1 + - + +
277A SER* 2.9 32.1 + - - -
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Residues in contact with MET 106 (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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44A VAL 4.3 1.8 - - - +
45A GLY* 3.8 8.7 - - - -
46A GLU* 3.3 36.3 - - + +
102A ALA* 3.1 20.5 + - + +
103A ALA 3.5 7.2 - - - +
105A GLU* 1.3 79.9 - - + +
107A ALA* 1.3 53.5 + - - +
109A LEU* 3.2 8.2 + - - +
110A ASP* 2.7 38.4 + - - +
120A ILE* 5.3 1.6 - - - +
270A LEU* 4.2 29.6 - - + -
271A CYS* 4.5 11.7 - - - -
275A GLY* 5.9 0.9 - - - -
276A VAL* 5.2 0.9 - - + -
303A ILE 4.8 0.7 - - - +
304A GLY* 4.7 16.6 - - - -
307A VAL* 4.1 36.1 - - + +
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Residues in contact with ALA 107 (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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34A VAL* 3.6 15.3 - - + +
36A VAL* 3.3 18.7 - - + +
43A GLY* 3.3 24.8 - - - +
44A VAL 4.0 7.0 - - - -
45A GLY* 4.1 2.1 - - - +
103A ALA 3.5 6.8 + - - +
104A VAL* 3.3 13.3 + - + +
106A MET* 1.3 79.8 - - - +
108A LEU* 1.3 57.4 + - - +
110A ASP* 3.4 1.6 + - - +
111A LEU* 2.9 31.2 + - - +
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Residues in contact with LEU 108 (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* 3.7 32.8 - - + -
6A ILE* 5.3 1.3 - - + -
36A VAL* 3.9 20.6 - - + -
75A LEU* 5.3 3.1 - - + -
79A ASP 6.1 0.4 - - - +
80A ALA* 4.2 25.0 - - + +
82A ASN 5.4 0.4 - - - +
83A VAL* 5.0 12.7 - - + +
86A ALA* 3.5 33.0 - - + -
90A MET* 4.8 2.7 - - + -
104A VAL* 3.3 26.0 + - + +
105A GLU* 3.9 6.5 - - - +
107A ALA* 1.3 75.9 - - - +
109A LEU* 1.3 57.4 + - - +
111A LEU* 4.0 5.5 - - + +
112A LYS* 3.1 30.1 + - - +
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Residues in contact with LEU 109 (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 VAL* 3.9 23.5 - - + +
105A GLU* 3.0 32.5 + - + +
106A MET* 3.4 6.5 - - - +
108A LEU* 1.3 76.0 - - - +
110A ASP* 1.3 63.7 + - - +
112A LYS* 4.1 4.2 - - + +
113A ALA* 3.1 24.6 + - - +
120A ILE* 4.6 21.3 - - + +
123A LEU* 4.0 20.6 - - + +
124A LEU* 5.2 7.2 - - + -
276A VAL* 3.8 38.1 - - + -
277A SER* 4.9 3.1 - - - +
307A VAL* 5.8 0.2 - - + -
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Residues in contact with ASP 110 (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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43A GLY* 3.5 2.1 - - - -
44A VAL* 2.7 30.6 + - - +
106A MET 2.7 16.9 + - - +
107A ALA 3.6 3.6 - - - +
109A LEU* 1.3 74.7 - - - +
111A LEU* 1.3 59.8 + - - +
113A ALA* 3.1 6.9 + - - +
114A ARG* 2.8 56.5 + - - +
120A ILE* 4.6 7.8 - - + +
307A VAL* 5.9 0.4 - - + -
353A GLY 3.2 3.8 - - - +
354A HIS* 2.7 38.7 + - + -
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Residues in contact with LEU 111 (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 MET* 3.7 29.8 - - - -
36A VAL* 3.5 34.5 - - + +
38A SER* 3.6 22.2 - - - -
41A LEU* 3.7 17.3 - - + +
42A VAL 3.9 13.2 - - - +
43A GLY* 3.9 3.8 - - - -
80A ALA* 4.7 12.6 - - + +
81A PHE* 4.2 9.0 - - + -
107A ALA 2.9 15.5 + - - +
108A LEU* 4.0 5.8 - - + +
110A ASP* 1.3 76.9 - - - +
112A LYS* 1.3 59.5 + - - +
114A ARG* 3.2 4.8 + - - +
115A ALA* 3.0 26.4 + - + +
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Residues in contact with LYS 112 (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 ALA 4.7 1.3 - - - +
81A PHE* 4.0 63.0 + - + +
83A VAL* 4.5 20.1 - - + +
108A LEU 3.1 16.1 + - - +
109A LEU* 4.1 4.0 - - - +
111A LEU* 1.3 80.0 - - - +
113A ALA* 1.3 61.6 + - - +
115A ALA* 3.5 2.4 + - - +
116A LEU* 3.3 38.7 + - + +
123A LEU* 4.6 21.0 - - + +
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Residues in contact with ALA 113 (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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109A LEU 3.1 20.1 + - - +
110A ASP 3.1 5.0 + - - +
112A LYS* 1.3 74.9 - - - +
114A ARG* 1.3 59.6 + - - +
116A LEU* 3.3 2.4 + - - -
117A GLY 3.1 17.5 + - - -
118A VAL* 3.0 31.7 + - + +
119A SER 4.2 1.8 - - - +
120A ILE* 4.2 11.9 - - - +
123A LEU* 4.1 15.5 - - + +
353A GLY* 4.0 18.2 - - - -
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Residues in contact with ARG 114 (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 LEU* 3.7 21.9 - - + +
42A VAL 4.3 14.1 - - - -
110A ASP* 2.8 42.7 + - - +
111A LEU 3.2 4.5 + - - +
113A ALA* 1.3 74.3 - - - +
115A ALA* 1.3 60.8 + - - +
117A GLY* 3.1 17.0 + - - -
352A VAL* 3.1 50.3 + - + +
353A GLY 3.1 13.9 + - - -
354A HIS* 4.0 1.6 + - - -
355A GLY* 3.9 1.4 - - - -
356A MET 3.2 36.8 + - - +
357A THR* 5.0 7.4 - - - +
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Residues in contact with ALA 115 (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 MET* 4.6 12.8 - - + -
41A LEU* 3.9 12.7 - - + +
81A PHE* 3.4 34.5 - - + -
111A LEU 3.0 15.2 + - - +
112A LYS 3.7 0.9 - - - +
113A ALA 3.3 0.2 - - - -
114A ARG* 1.3 76.3 - - - +
116A LEU* 1.3 62.4 + - - +
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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