Contacts of the helix formed by residues 98 - 112 (chain B) in PDB entry 2C4P
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 THR 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG* 3.9 5.2 - - - -
9B GLU* 2.6 37.7 + - - +
60B TYR* 4.4 1.6 - - - -
93B TRP* 5.3 0.2 - - - -
96B ALA 4.4 1.8 - - - +
97B LEU* 1.3 76.3 - - - +
99B VAL* 1.3 65.2 + - - +
100B SER* 3.3 22.9 + - - +
101B LYS* 2.9 39.6 + - + +
102B VAL* 2.9 18.1 + - - +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU* 2.5 36.7 + - + +
13B LEU* 5.3 1.3 - - + -
23B ALA* 5.9 2.9 - - + -
33B TRP* 4.8 15.5 - - + -
54B VAL* 3.6 35.4 - - + -
56B PHE* 3.9 21.5 - - + -
60B TYR* 3.6 11.3 + - - +
65B PRO* 4.6 7.9 - - + -
67B ILE* 5.7 0.4 - - + -
98B THR* 1.3 71.5 + - - +
100B SER* 1.3 64.2 + - - +
102B VAL* 2.8 23.0 + - + +
103B LEU* 3.1 11.3 + - - +
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 4.0 38.5 - - - +
18B PRO* 5.9 6.7 - - - -
23B ALA* 6.3 1.1 - - - -
98B THR* 3.3 21.2 + - - +
99B VAL* 1.3 76.6 - - - +
101B LYS* 1.3 54.6 + - - +
103B LEU* 3.3 20.3 + - - +
104B LEU* 2.6 27.4 - - - +
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Residues in contact with LYS 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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1A MET* 6.2 3.8 - - - -
88B ILE* 5.6 0.7 - - + -
96B ALA* 4.6 10.9 + - - +
97B LEU* 3.7 30.7 - - + +
98B THR* 2.9 35.1 + - + +
100B SER* 1.3 77.4 + - - +
102B VAL* 1.3 52.3 + - + +
103B LEU 2.9 3.8 - - - -
104B LEU* 2.7 44.3 + - + +
105B SER* 3.2 9.7 + - - +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PRO* 5.3 4.3 - - + -
67B ILE* 4.2 15.3 - - + -
86B LEU* 3.9 20.6 - - + -
88B ILE* 3.6 23.6 - - + -
89B LEU* 4.0 19.5 - - + -
93B TRP* 4.4 13.7 - - + -
98B THR 3.1 20.4 - - - +
99B VAL* 2.8 13.9 + - + +
101B LYS* 1.3 73.4 - - - +
103B LEU* 1.3 58.2 + - - +
104B LEU 3.3 0.2 - - - -
105B SER* 3.5 10.1 - - - -
106B ILE* 3.2 24.1 + - - +
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Residues in contact with LEU 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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18B PRO* 6.1 0.7 - - + -
21B CYS* 3.5 29.7 - - + -
22B SER 4.1 18.4 - - - +
23B ALA* 4.7 9.0 - - + -
35B ALA* 4.4 14.4 - - + -
37B ILE* 3.5 27.4 - - + +
52B LEU* 4.9 5.8 - - + -
67B ILE* 6.0 1.1 - - + -
99B VAL 3.1 8.3 + - - +
100B SER* 3.4 15.3 - - - +
101B LYS 2.9 0.4 - - - -
102B VAL* 1.3 75.7 - - - +
104B LEU* 1.3 63.6 + - + +
105B SER 3.2 0.4 - - - -
106B ILE* 3.3 20.0 + - + +
107B CYS* 3.0 28.6 + - - +
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Residues in contact with LEU 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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1A MET* 5.4 4.3 - - + -
62A PHE* 3.1 44.6 - - + -
18B PRO* 5.4 9.2 - - + -
21B CYS* 4.6 15.9 - - + -
100B SER* 2.6 31.6 - - - +
101B LYS* 2.7 29.3 + - + +
103B LEU* 1.3 75.3 - - + +
105B SER* 1.3 61.3 + - - +
107B CYS* 3.4 1.2 + - - -
108B SER* 2.8 28.1 + - - -
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Residues in contact with SER 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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1A MET* 4.1 20.3 - - - +
86B LEU* 4.2 22.7 - - - +
88B ILE* 4.4 11.4 - - - +
101B LYS* 3.2 11.2 + - - +
102B VAL* 3.5 14.2 - - - -
104B LEU* 1.3 77.3 - - - +
106B ILE* 1.3 59.2 + - - +
108B SER* 3.3 7.3 + - - -
109B LEU* 2.8 30.7 + - - +
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Residues in contact with ILE 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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37B ILE* 5.5 6.1 - - + -
52B LEU* 4.8 11.0 - - + -
67B ILE* 3.6 31.6 - - + -
69B PHE* 3.4 31.0 - - + -
84B ILE* 3.4 23.8 - - + -
86B LEU* 4.1 4.9 - - + -
102B VAL* 3.2 15.6 + - + +
103B LEU* 3.6 24.2 - - + +
104B LEU 3.3 0.2 - - - -
105B SER* 1.3 73.6 - - - +
107B CYS* 1.3 60.6 + - - +
109B LEU* 3.2 9.7 + - + +
110B LEU* 2.9 38.4 + - + +
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Residues in contact with CYS 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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62A PHE* 4.6 10.3 - - + -
95A PRO* 5.6 10.9 - - + +
20B HIS* 3.8 31.6 - - - -
21B CYS* 4.8 10.8 - - - -
37B ILE* 5.0 6.7 - - + +
38B MET 4.2 6.1 - - - -
40B PRO* 4.1 17.5 - - - +
103B LEU 3.0 17.6 + - - +
104B LEU* 3.7 7.2 - - - +
105B SER 3.3 0.2 - - - -
106B ILE* 1.3 77.1 - - - +
108B SER* 1.3 61.5 + - - +
110B LEU* 3.4 26.0 - - - +
111B CYS* 3.7 4.2 + - - +
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Residues in contact with SER 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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1A MET* 4.8 7.8 - - - +
5A ARG* 3.9 18.0 + - - +
61A PRO* 4.2 14.6 - - - +
62A PHE* 3.3 17.8 - - - -
95A PRO* 5.4 6.8 - - - +
104B LEU 2.8 19.1 + - - -
105B SER* 3.5 9.9 - - - -
107B CYS* 1.3 73.8 - - - +
109B LEU* 1.3 66.5 - - - +
110B LEU 3.0 1.1 - - - -
111B CYS* 2.9 16.6 + - - +
112B ASP 2.9 12.2 + - - -
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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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75B HIS* 2.9 27.7 + - + +
77B ASN* 3.6 22.0 - - + +
78B ILE* 4.8 2.0 - - + -
84B ILE* 4.1 25.1 - - + -
85B CYS 4.2 9.0 - - - +
86B LEU* 4.0 24.9 - - + -
105B SER 2.8 17.7 + - - +
106B ILE* 3.5 6.7 - - + +
108B SER* 1.3 76.1 - - - +
110B LEU* 1.3 64.4 + - + +
112B ASP 3.9 8.1 - - - +
113B PRO* 3.2 32.0 - - + -
114B ASN* 4.3 11.9 - - - +
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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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37B ILE* 4.3 22.4 - - + -
38B MET 5.2 0.9 - - - +
39B GLY* 5.3 1.8 - - - -
40B PRO* 4.5 12.8 - - + -
45B TYR* 3.0 45.0 + - + -
50B PHE* 5.5 5.4 - - + -
69B PHE* 4.2 26.7 - - + -
73B ILE* 5.2 6.3 - - + -
75B HIS* 3.2 20.9 - - + +
78B ILE* 5.7 1.8 - - + -
106B ILE* 2.9 25.9 + - + +
107B CYS* 3.4 28.3 - - - +
108B SER 3.0 0.4 - - - -
109B LEU* 1.3 80.0 - - + +
111B CYS* 1.3 61.7 + - - +
113B PRO* 4.0 0.7 - - - +
134B TYR* 5.2 1.9 + - - -
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Residues in contact with CYS 111 (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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5A ARG* 4.6 3.4 - - - +
95A PRO* 5.1 1.1 - - + -
96A ALA* 3.1 52.9 - - + +
40B PRO* 5.0 2.9 - - + +
42B ASP 5.2 0.7 - - - -
43B SER* 4.5 13.7 - - - -
45B TYR* 5.2 0.7 - - - -
107B CYS 3.7 5.0 + - - +
108B SER* 2.9 9.4 + - - +
110B LEU* 1.3 81.7 - - - +
112B ASP* 1.3 68.1 + - - +
113B PRO* 3.1 10.4 - - - +
127B TYR* 4.3 4.2 + - - -
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Residues in contact with ASP 112 (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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5A ARG* 2.9 45.0 + - - +
8A LYS* 5.4 13.7 - - + +
9A GLU* 4.3 9.3 - - - +
12A ASP* 5.5 6.4 - - - +
15A ARG* 6.0 0.2 + - - -
96A ALA 4.6 1.7 - - - +
98A THR* 4.8 5.4 - - - +
108B SER 2.9 6.3 + - - -
109B LEU* 3.4 14.7 - - - +
111B CYS* 1.3 85.5 - - - +
113B PRO* 1.3 64.1 - - - +
127B TYR* 4.0 9.7 + - - +
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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