Contacts of the helix formed by residues 95 - 110 (chain B) in PDB entry 2JDQ
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 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B SER* 3.4 1.5 + - - -
94B LYS* 1.3 79.6 - - - +
96B PRO* 1.4 67.4 - - - +
97B GLU* 3.4 7.9 + - - +
98B GLN* 3.3 37.7 + - - +
99B GLN* 3.0 27.2 + - - +
137B ARG* 5.1 0.2 - - - -
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Residues in contact with PRO 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LYS 4.3 3.6 - - - +
95B SER* 1.4 82.7 - - - +
97B GLU* 1.3 70.4 + - + +
98B GLN 3.5 0.2 - - - -
99B GLN* 3.6 12.9 - - - +
100B LEU* 3.3 24.4 + - - +
137B ARG* 4.1 21.8 - - - +
140B ASN* 4.5 14.8 + - - +
143B LEU* 5.1 1.3 - - + +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B SER* 3.3 7.7 - - - +
96B PRO* 1.3 84.0 - - + +
98B GLN* 1.3 65.9 + - + +
100B LEU* 4.1 2.6 - - - +
101B SER* 3.1 25.0 + - - -
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Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B MET* 3.8 40.4 - - + +
93B SER* 3.0 30.3 + - - +
95B SER* 3.3 17.3 + - - +
97B GLU* 1.3 83.9 - - + +
99B GLN* 1.3 57.7 + - - +
101B SER* 3.7 6.3 - - - -
102B ALA* 3.0 31.4 + - - +
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B MET 3.8 8.5 - - - +
91B ILE* 3.6 19.8 - - - +
93B SER 2.5 26.1 + - - -
94B LYS* 4.0 4.0 - - - +
95B SER 3.0 22.9 + - - +
96B PRO* 3.6 3.9 - - - +
97B GLU 3.2 0.6 - - - -
98B GLN* 1.3 76.2 - - - +
100B LEU* 1.3 57.7 + - - +
102B ALA* 3.5 3.2 + - - +
103B THR* 2.6 38.0 + - - -
130B ARG* 3.4 11.5 - - - +
134B PHE* 3.4 22.9 - - + -
137B ARG* 2.5 33.6 + - - +
143B LEU* 4.0 4.6 - - + +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B PRO 3.3 15.0 + - - +
97B GLU* 4.1 2.9 - - - +
99B GLN* 1.3 75.1 - - - +
101B SER* 1.3 61.7 - - - +
103B THR* 3.3 1.0 + - - -
104B GLN* 2.9 48.0 + - + +
140B ASN* 4.0 14.8 - - - +
142B THR* 3.3 45.3 - - + +
143B LEU* 3.7 24.3 - - + +
146B GLU* 3.9 10.5 - - + -
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Residues in contact with SER 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B MET* 5.0 7.8 - - - -
97B GLU 3.1 17.2 + - - -
98B GLN* 3.7 7.6 - - - -
100B LEU* 1.3 77.8 - - - +
102B ALA* 1.3 62.2 + - - +
104B GLN* 3.2 16.2 + - - +
105B LYS* 3.2 26.8 + - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B MET* 4.3 21.1 - - - +
90B MET* 4.0 22.0 - - + -
91B ILE* 4.3 8.7 - - + +
98B GLN 3.0 20.7 + - - +
99B GLN 4.0 2.7 - - - +
101B SER* 1.3 74.9 + - - +
103B THR* 1.3 58.0 + - - +
104B GLN 3.4 0.2 - - - -
105B LYS* 3.5 13.3 + - + +
106B PHE* 3.0 32.8 + - + -
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ILE* 4.7 2.4 - - - +
99B GLN 2.6 23.1 + - - -
100B LEU 3.7 5.2 - - - -
101B SER 3.2 0.2 - - - -
102B ALA* 1.3 75.6 - - - +
104B GLN* 1.3 58.9 + - - +
105B LYS 3.2 0.2 - - - -
106B PHE* 3.3 8.1 + - - +
107B ARG* 3.0 27.0 + - - +
131B PHE* 4.3 14.8 - - + -
134B PHE* 4.0 13.0 - - - -
143B LEU* 3.9 12.2 - - + +
146B GLU* 3.7 30.2 - - + +
147B SER* 3.8 19.7 - - - +
150B VAL* 4.2 1.5 - - + +
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 2.9 36.0 + - - +
101B SER* 3.6 13.5 - - - +
103B THR* 1.3 74.4 - - - +
105B LYS* 1.3 62.0 + - - +
107B ARG* 3.7 14.0 + - - +
108B LYS* 3.5 28.8 + - - +
142B THR* 4.1 11.5 - - - +
146B GLU* 3.5 32.3 + - + +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B THR* 4.7 12.7 + - - +
86B ASP* 4.9 15.2 + - + +
87B MET* 4.8 20.4 - - + -
101B SER* 3.2 17.7 + - - +
102B ALA* 3.5 12.8 - - - +
104B GLN* 1.3 74.1 - - - +
106B PHE* 1.3 64.7 + - - +
107B ARG 3.1 0.2 - - - -
108B LYS* 3.0 28.9 + - + +
109B LEU* 3.4 11.8 + - - +
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B MET* 3.4 53.4 - - + -
88B ILE* 5.5 4.5 - - + -
91B ILE* 3.9 23.3 - - + -
102B ALA 3.0 23.7 + - - +
103B THR* 3.3 10.5 + - - +
105B LYS* 1.3 75.1 - - - +
107B ARG* 1.3 61.3 + - - +
109B LEU* 3.5 19.7 + - + +
110B LEU* 3.7 16.3 + - + +
121B VAL* 4.4 32.8 - - + -
124B THR* 5.8 3.6 - - + -
127B VAL* 4.7 12.8 - - + -
131B PHE* 3.9 26.2 - + + -
150B VAL* 4.2 9.2 - - + +
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B THR 3.0 16.9 + - - +
104B GLN* 3.7 14.6 + - - +
105B LYS 3.1 0.4 - - - -
106B PHE* 1.3 77.5 - - - +
108B LYS* 1.3 85.0 + - - +
110B LEU* 3.4 5.3 + - - +
111B SER* 2.7 33.8 + - - +
146B GLU* 3.1 36.5 + - - +
149B TRP* 3.2 62.8 - - + -
150B VAL* 3.9 13.6 - - + +
153B ASN* 4.9 0.9 + - - +
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLN* 3.5 17.2 + - - +
105B LYS* 3.0 19.7 + - + +
107B ARG* 1.3 98.0 - - - +
109B LEU* 1.3 66.1 + - - +
111B SER* 3.4 14.6 + - - -
112B LYS* 3.6 29.0 + - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B MET* 4.0 30.3 - - + -
105B LYS 3.4 7.9 + - - +
106B PHE* 3.7 18.2 - - + +
107B ARG 3.3 0.6 - - - -
108B LYS* 1.3 80.6 - - - +
110B LEU* 1.3 62.7 + - + +
111B SER 3.8 0.5 + - - -
112B LYS* 4.5 25.2 + - + +
116B PRO* 4.0 2.9 - - - +
117B PRO* 3.3 49.0 - - + +
121B VAL* 5.5 4.3 - - + -
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PHE* 3.7 10.7 + - + +
107B ARG* 3.4 7.1 + - - +
108B LYS 3.3 0.4 - - - -
109B LEU* 1.3 77.0 - - + +
111B SER* 1.3 56.0 + - - +
112B LYS 3.7 1.6 - - - +
116B PRO* 3.8 24.7 - - + +
117B PRO* 3.6 36.8 - - + +
118B ILE* 3.9 9.6 - - + +
121B VAL* 4.2 13.9 - - + -
150B VAL* 4.1 26.2 - - + +
153B ASN* 2.7 40.5 + - + +
154B ILE* 3.9 27.1 - - + +
754D ILE* 4.2 7.1 - - - +
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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