Contacts of the helix formed by residues 85 - 101 (chain A) in PDB entry 2JDC
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 LYS 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ILE* 4.8 0.7 - - - -
83A GLU 3.5 6.0 + - - +
84A GLN* 1.3 79.4 - - - +
86A ALA* 1.3 56.3 + - - +
87A GLY 3.4 1.6 - - - -
88A SER* 3.9 20.2 - - - +
89A SER* 2.6 43.8 + - - +
1147A CAO 2.9 62.4 + - - +
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Residues in contact with ALA 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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2A ILE* 3.9 23.7 - - + +
51A ILE* 3.7 29.8 - - + -
52A SER* 3.8 12.8 - - - -
77A THR* 4.3 3.8 - - + -
81A TYR 4.4 4.5 - - - +
84A GLN* 3.2 3.6 + - - +
85A LYS* 1.3 77.8 - - - +
87A GLY* 1.3 64.4 + - - +
89A SER* 3.2 2.6 + - - -
90A LEU* 3.1 26.5 + - - +
1147A CAO 3.7 10.0 + - - +
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Residues in contact with GLY 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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52A SER* 3.8 2.6 + - - -
75A MET* 3.7 18.1 - - - +
77A THR* 4.2 0.9 - - - -
85A LYS 3.4 0.2 - - - -
86A ALA* 1.3 75.5 - - - +
88A SER* 1.3 62.9 - - - +
90A LEU* 3.1 5.6 + - - +
91A ILE* 3.0 19.4 + - - +
117A TYR* 2.9 24.1 + - - -
1147A CAO 3.0 19.5 + - - -
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS* 3.9 19.0 - - - +
86A ALA 3.4 0.2 - - - -
87A GLY* 1.3 73.3 - - - +
89A SER* 1.3 57.7 + - - +
91A ILE* 3.3 1.6 + - - +
92A LYS* 2.9 43.4 + - - +
117A TYR* 3.4 3.5 + - - -
121A LEU* 3.6 28.3 - - - +
1147A CAO 2.6 38.5 + - - -
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Residues in contact with SER 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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2A ILE* 4.6 10.2 - - - +
4A VAL* 3.8 22.0 - - - +
85A LYS* 2.6 29.5 + - - +
86A ALA* 3.2 6.3 + - - -
88A SER* 1.3 75.6 - - - +
90A LEU* 1.3 63.9 + - - +
92A LYS* 3.5 6.1 + - - +
93A HIS* 3.0 25.3 + - - +
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Residues in contact with LEU 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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4A VAL* 3.7 22.2 - - + -
42A LEU* 3.4 24.6 - - + +
43A GLY 3.5 26.0 - - - +
44A GLY* 3.6 5.4 - - - +
52A SER* 3.5 23.8 - - - +
53A ILE 3.6 31.2 - - - +
54A ALA* 3.8 11.4 - - + +
56A PHE* 5.0 0.9 - - - -
75A MET* 4.3 2.2 - - + -
86A ALA 3.1 17.6 + - - +
87A GLY* 3.1 6.7 + - - +
89A SER* 1.3 77.3 - - - +
91A ILE* 1.3 55.9 + - - +
93A HIS* 4.6 0.7 - - - -
94A ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 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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54A ALA* 4.9 0.4 - - + -
56A PHE* 4.0 17.9 - - + -
72A LEU* 3.6 31.2 - - + -
75A MET* 3.9 9.9 - - - -
87A GLY 3.0 16.0 + - - +
88A SER 3.8 3.8 - - - +
90A LEU* 1.3 76.4 - - - +
92A LYS* 1.3 56.6 + - - +
94A ALA* 3.2 4.0 + - - +
95A GLU* 2.8 54.1 + - - +
106A LEU* 4.4 7.6 - - + -
117A TYR* 3.7 13.5 - - + +
118A TYR* 5.1 2.2 - - + -
121A LEU* 4.0 25.6 - - + -
123A PHE* 4.3 10.8 - - + -
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Residues in contact with LYS 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 SER* 2.9 26.6 + - - +
89A SER* 4.0 5.8 - - - +
91A ILE* 1.3 75.0 - - - +
93A HIS* 1.3 62.5 + - - +
95A GLU* 3.2 20.2 + - - +
96A GLU* 3.2 26.6 + - - +
121A LEU* 4.6 18.6 - - + -
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Residues in contact with HIS 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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4A VAL* 3.7 33.6 - - + +
5A LYS 6.2 0.4 - - - -
6A PRO* 6.2 2.0 - - - +
42A LEU* 3.9 16.7 - - + +
89A SER 3.0 17.5 + - - +
90A LEU 3.7 3.4 - - - +
92A LYS* 1.3 75.5 - - - +
94A ALA* 1.3 63.0 + - - +
96A GLU* 3.2 31.3 + - - +
97A ILE* 3.3 31.3 + - + +
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Residues in contact with ALA 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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40A PHE* 4.3 7.6 - - + -
42A LEU* 3.7 7.8 - - + +
56A PHE* 3.2 49.6 - - + -
90A LEU 2.9 14.4 + - - +
91A ILE 3.5 4.3 - - - +
93A HIS* 1.3 78.1 - - - +
95A GLU* 1.3 56.8 + - + +
97A ILE* 3.1 4.0 + - - +
98A LEU* 2.8 36.0 + - + +
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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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91A ILE* 2.8 38.1 + - + +
92A LYS* 3.2 24.4 + - - +
94A ALA* 1.3 76.8 - - - +
96A GLU* 1.3 56.5 + - - +
98A LEU* 3.9 6.9 - - + +
99A ARG* 2.8 58.8 + - - +
106A LEU* 4.4 13.5 - - + +
121A LEU* 4.8 1.6 - - - +
123A PHE* 4.5 0.2 - - - -
143A LYS* 3.4 35.5 - - - +
145A ILE* 4.3 14.3 - - + +
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Residues in contact with GLU 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 LYS* 3.2 15.2 + - - +
93A HIS* 3.2 26.5 + - + +
95A GLU* 1.3 75.5 - - - +
97A ILE* 1.3 64.5 + - + +
99A ARG* 3.9 8.5 - - - +
100A LYS* 3.0 25.6 + - - +
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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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40A PHE* 3.7 39.9 - - + -
42A LEU* 4.3 7.0 - - + -
93A HIS* 3.3 35.6 + - + +
94A ALA* 3.1 7.0 + - - +
96A GLU* 1.3 76.5 - - + +
98A LEU* 1.3 62.7 + - - +
100A LYS* 3.3 8.7 + - - +
101A ARG* 3.0 46.0 + - - +
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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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40A PHE* 3.7 20.2 - - + -
56A PHE* 4.5 5.8 - - + -
70A TYR* 3.4 47.8 - - + -
94A ALA 2.8 24.6 + - - +
95A GLU* 3.9 2.7 - - - +
97A ILE* 1.3 74.6 - - + +
99A ARG* 1.3 65.4 + - - +
101A ARG* 3.1 11.5 + - - +
103A ALA* 3.0 29.4 + - + +
105A LEU 5.3 0.2 - - - +
106A LEU* 3.9 40.4 - - + -
145A ILE* 3.7 17.5 - - + -
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Residues in contact with ARG 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 GLU* 2.8 46.6 + - - +
96A GLU* 3.9 8.7 - - - +
98A LEU* 1.3 72.8 - - - +
100A LYS* 1.3 62.2 + - - +
102A GLY* 3.0 14.0 + - - -
103A ALA 4.6 6.3 - - - +
143A LYS* 4.5 11.9 - - - +
144A ARG 4.6 0.8 + - - -
145A ILE* 2.9 58.1 + - + +
146A THR 5.4 1.4 + - - -
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Residues in contact with LYS 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 GLU 3.0 18.6 + - - +
97A ILE* 3.6 8.3 - - - +
98A LEU 3.2 0.2 - - - -
99A ARG* 1.3 76.4 - - - +
101A ARG* 1.3 60.9 + - + +
102A GLY 3.2 0.7 + - - -
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Residues in contact with ARG 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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38A GLY* 2.9 31.9 + - - -
39A ALA 5.3 0.4 + - - -
40A PHE* 3.7 30.4 - - - +
68A LYS* 3.6 25.1 - - - +
70A TYR* 2.9 29.0 + - + +
97A ILE* 3.0 31.5 + - + +
98A LEU* 3.1 11.6 + - - +
100A LYS* 1.3 76.7 - - + +
102A GLY* 1.3 59.9 + - - +
103A ALA 3.6 0.8 + - - +
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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