Contacts of the helix formed by residues 100 - 112 (chain A) in PDB entry 1JID
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 SER 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.8 10.7 - - - +
98A PHE 3.2 1.6 + - - -
99A PRO* 1.3 87.1 - - - +
101A ARG* 1.3 66.0 + - - +
102A LYS* 3.5 10.0 + - - +
103A SER* 2.7 44.9 + - - -
104A VAL* 3.3 10.0 + - - +
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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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16A ILE* 3.6 41.2 - - + +
17A CYS 5.6 2.7 - - - +
18A ILE* 5.2 0.8 - - + +
86A LEU* 3.8 9.1 - - + +
100A SER* 1.3 74.3 - - - +
102A LYS* 1.3 64.6 + - - +
104A VAL* 3.1 5.4 + - - +
105A MET* 2.9 36.5 + - + +
147B G 3.2 55.1 + - - +
148B G 3.0 35.2 + - - -
149B A 2.8 40.4 + - - -
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Residues in contact with LYS 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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34A ARG* 2.9 28.7 + - - +
35A ILE* 3.7 7.7 - - - +
36A PRO* 5.6 1.2 - - - +
100A SER* 3.2 9.5 + - - +
101A ARG* 1.3 80.7 - - - +
103A SER* 1.3 62.5 + - - +
105A MET* 3.1 31.2 + - + +
106A LEU* 2.9 43.3 + - + +
144B C 4.0 21.8 - - - +
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Residues in contact with SER 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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97A GLN 4.1 7.6 - - - -
98A PHE* 3.2 26.1 - - - -
99A PRO* 3.7 15.7 - - - -
100A SER* 2.7 35.0 + - - -
102A LYS* 1.3 77.0 - - - +
104A VAL* 1.3 59.4 + - - +
106A LEU* 4.1 8.0 - - - +
107A TYR* 3.1 24.4 + - - +
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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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16A ILE* 5.0 1.6 - - + -
18A ILE* 3.4 27.1 - - + -
53A CYS* 3.7 22.0 - - - -
58A LEU* 4.1 13.9 - - + -
84A VAL* 4.4 8.3 - - + -
86A LEU* 3.9 21.8 - - + -
98A PHE* 3.8 24.2 - - + -
100A SER 3.6 12.3 - - - +
101A ARG* 3.1 9.5 + - - +
103A SER* 1.3 75.0 + - - +
105A MET* 1.3 65.9 + - - +
107A TYR* 3.3 2.5 + - + +
108A ALA* 2.9 22.9 + - - +
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Residues in contact with MET 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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18A ILE* 4.3 20.0 - - + -
22A TYR* 3.8 24.0 - - - -
23A LEU* 3.5 24.0 - - + +
34A ARG* 3.7 27.1 - - + -
35A ILE* 3.9 7.0 - - + -
101A ARG* 2.9 19.6 + - + +
102A LYS* 3.1 48.0 + - + +
104A VAL* 1.3 77.7 - - - +
106A LEU* 1.3 61.8 + - - +
108A ALA* 3.5 2.5 + - - -
109A ALA* 3.0 24.3 + - - +
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Residues in contact with LEU 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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35A ILE* 3.6 28.9 - - + -
36A PRO* 4.5 2.5 - - + -
39A LYS* 3.5 47.5 - - + +
102A LYS* 2.9 37.1 + - + +
103A SER* 4.1 6.3 - - - +
105A MET* 1.3 75.3 - - - +
107A TYR* 1.3 64.8 + - - +
109A ALA* 3.2 4.9 + - - +
110A GLU* 2.9 25.7 + - - +
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Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A VAL 3.7 24.9 + - - -
53A CYS* 5.3 4.5 - - - -
55A ALA* 5.6 1.2 - - - +
56A VAL* 3.5 29.3 + - + +
58A LEU* 5.8 0.2 - - + -
97A GLN* 4.0 25.4 - - - -
98A PHE* 3.5 19.5 - + + -
103A SER 3.1 19.0 + - - +
104A VAL 3.6 3.4 - - - +
105A MET 3.3 0.2 - - - -
106A LEU* 1.3 77.6 - - - +
108A ALA* 1.3 67.9 + - + +
110A GLU* 3.0 21.1 + - - +
111A MET* 3.0 61.3 + - + +
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Residues in contact with ALA 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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18A ILE* 5.7 0.9 - - + -
23A LEU* 3.9 19.1 - - + -
49A ILE* 4.4 7.9 - - + -
52A VAL* 3.6 27.1 - - + -
53A CYS* 4.3 12.1 - - - -
104A VAL* 2.9 17.1 + - + +
105A MET* 4.7 0.7 - - - -
107A TYR* 1.3 77.5 - - - +
109A ALA* 1.3 63.6 + - - +
111A MET 3.1 0.9 + - - -
112A ILE* 2.9 33.4 + - + +
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Residues in contact with ALA 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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23A LEU* 4.3 9.3 - - + +
35A ILE* 3.5 18.4 - - + -
39A LYS* 3.3 25.3 - - + +
40A ALA* 4.6 0.2 - - - -
41A VAL* 3.1 22.5 - - + +
105A MET 3.0 18.7 + - - +
106A LEU* 3.6 4.7 - - - +
107A TYR 3.2 0.2 - - - -
108A ALA* 1.3 77.1 - - - +
110A GLU* 1.3 57.9 + - - +
112A ILE* 5.0 0.4 - - - -
113A PRO* 3.0 23.9 - - - +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LYS 5.5 0.2 - - - -
106A LEU 2.9 12.0 + - - +
107A TYR* 3.3 28.2 - - - +
109A ALA* 1.3 78.0 - - - +
111A MET* 1.3 61.0 + - + +
113A PRO* 3.2 14.2 - - - +
114A LYS* 3.9 30.4 - - - +
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Residues in contact with MET 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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52A VAL* 3.8 22.6 - - + +
107A TYR* 3.0 57.2 + - + +
108A ALA 4.0 0.2 - - - +
110A GLU* 1.3 83.6 - - + +
112A ILE* 1.3 66.3 + - - +
114A LYS* 2.8 52.8 + - + +
115A LEU* 3.4 5.9 + - - +
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Residues in contact with ILE 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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23A LEU* 4.4 7.0 - - + -
41A VAL* 4.5 10.5 - - + -
44A PRO* 4.1 14.6 - - + -
48A GLU* 3.8 25.1 - - + +
49A ILE* 3.7 31.4 - - + +
52A VAL* 4.0 16.4 - - + -
108A ALA 2.9 20.9 + - - +
109A ALA 4.5 1.3 - - - +
111A MET* 1.3 75.9 - - - +
113A PRO* 1.4 68.6 - - + +
115A LEU* 3.1 21.8 + - + +
118A ARG* 3.4 40.4 - - - +
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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