Contacts of the strand formed by residues 6 - 19 (chain T) in PDB entry 5HJD
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 6 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4Q SER 3.2 11.1 - - - +
6Q ALA* 3.5 30.5 + - + +
5T CYS* 1.3 73.9 - - - +
7T VAL* 1.3 63.1 + - - +
8T GLN* 3.5 9.9 + - + +
123T THR* 4.5 14.1 - - + -
124T PHE 3.7 6.1 - - - -
125T ASN* 4.6 7.0 - - - +
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Residues in contact with VAL 7 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q SER 3.3 9.4 - - - +
5Q CYS* 4.3 6.7 - - + -
5T CYS* 3.6 25.1 - - - -
6T ALA* 1.3 70.1 - - - +
8T GLN* 1.3 67.1 + - - +
9T VAL* 4.7 1.6 - - + -
122T LEU 3.6 0.9 - - - +
123T THR* 3.5 1.0 - - - -
124T PHE* 2.8 41.8 + - + +
127T PRO* 3.8 19.5 - - + -
132T ARG* 4.9 10.1 - - + +
135T LEU* 3.8 39.3 - - + -
136T LEU* 4.5 13.5 - - + -
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Residues in contact with GLN 8 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K LYS* 5.8 1.7 + - - -
2Q ALA 3.8 0.9 - - - +
3Q SER* 3.1 26.3 - - - -
4Q SER* 3.2 21.9 + - - +
6T ALA* 4.0 11.0 - - + +
7T VAL* 1.3 75.2 - - - +
9T VAL* 1.3 63.3 + - - +
10T LYS* 5.9 0.7 - - + -
121T LYS* 3.4 43.1 + - + +
122T LEU 3.1 5.8 - - - +
123T THR* 3.4 26.2 + - + +
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Residues in contact with VAL 9 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q ALA 3.8 4.5 - - - +
3Q SER* 3.9 7.2 - - - -
7T VAL* 4.7 1.1 - - + -
8T GLN* 1.3 79.1 - - - +
10T LYS* 1.3 64.4 + - - +
47T PHE* 3.8 31.9 - - + -
120T GLU 4.2 0.2 - - - +
121T LYS* 3.7 2.8 - - - +
122T LEU* 2.8 51.2 + - + +
124T PHE* 3.9 15.3 - - + -
135T LEU* 3.6 41.1 - - + +
138T ALA* 5.2 1.6 - - + -
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Residues in contact with LYS 10 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119K CYS 5.8 2.4 + - - -
1Q MET* 4.8 14.6 - - - +
2Q ALA* 3.7 33.9 + - + +
8T GLN 5.9 0.4 - - - -
9T VAL* 1.3 79.1 - - - +
11T LEU* 1.3 71.6 + - - +
38T GLY* 4.1 2.9 - - - -
39T PRO* 3.4 33.4 - - + +
42T SER* 5.2 0.3 + - - -
44T ILE* 4.3 4.3 - - - +
120T GLU 3.7 4.9 - - - +
121T LYS* 4.3 31.2 - - + +
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Residues in contact with LEU 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T LYS* 1.3 83.9 - - - +
12T GLU* 1.3 63.2 + - - +
13T LEU* 4.1 11.2 - - + -
36T VAL* 4.5 8.5 - - + -
37T ARG 3.6 8.1 - - - +
39T PRO* 4.3 2.4 - - - +
44T ILE* 3.7 34.5 - - + -
47T PHE* 4.4 8.7 - - + -
48T VAL* 5.2 1.1 - - + -
87T VAL* 4.4 27.6 - - + -
100T PHE* 4.5 11.7 - - + -
118T ARG 3.8 1.2 - - - +
119T CYS* 3.9 2.4 - - - -
120T GLU* 2.8 42.0 + - + +
122T LEU* 3.7 31.4 - - + -
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Residues in contact with GLU 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116K HIS* 6.0 1.2 - - - -
117K LEU* 4.2 21.5 + - + +
11T LEU* 1.3 76.3 - - - +
13T LEU* 1.3 63.0 + - - +
35T PHE* 4.0 3.0 - - + +
36T VAL* 3.4 4.7 - - - +
37T ARG* 2.6 82.8 + - + +
39T PRO* 3.8 32.7 - - + +
40T GLU 5.2 0.7 + - - -
117T LEU* 4.6 16.0 - - + +
118T ARG 3.5 8.3 - - - +
119T CYS* 5.4 7.5 - - - -
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Residues in contact with LEU 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T LEU* 4.2 15.7 - - + -
12T GLU* 1.3 79.1 - - - +
14T GLY* 1.3 56.5 + - - +
35T PHE* 3.6 4.7 - - - +
36T VAL* 3.9 22.0 - - + -
85T ILE* 3.9 21.1 - - + -
100T PHE* 3.8 40.4 - - + -
102T TYR* 3.9 19.7 - - + -
117T LEU* 3.5 3.1 - - - +
118T ARG* 2.6 55.3 + - + +
120T GLU* 4.1 19.5 - - + -
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Residues in contact with GLY 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T LEU* 1.3 75.0 - - - +
15T HIS* 1.3 62.2 + - - +
34T VAL* 3.5 3.5 - - - +
35T PHE* 2.9 49.5 + - - -
102T TYR* 3.1 17.0 - - - -
116T HIS 3.2 12.8 - - - -
117T LEU* 4.1 0.7 - - - -
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Residues in contact with HIS 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T GLY* 1.3 76.3 - - - +
16T ARG* 1.3 65.4 + - - +
17T ALA* 4.1 13.9 - - + -
32T TRP* 5.2 0.7 - - + -
33T MET 3.1 14.4 - - - +
34T VAL* 3.8 10.3 - - + -
35T PHE* 3.8 5.0 - - - -
102T TYR* 2.6 36.0 + + + +
103T ASP 3.9 6.7 - - - -
104T LEU* 3.9 17.5 - - + -
105T PHE* 3.0 57.6 + + - -
114T VAL* 3.3 16.5 - - + +
115T ASN* 3.9 0.9 - - - -
116T HIS* 3.2 29.5 + - + +
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Residues in contact with ARG 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115K ASN* 5.6 7.1 - - - +
15T HIS* 1.3 75.8 - - - +
17T ALA* 1.3 62.3 + - - +
18T GLN 5.7 0.2 - - - +
31T ASP 4.6 0.4 - - - -
32T TRP* 3.1 6.5 - - - +
33T MET* 2.8 64.7 + - + +
35T PHE* 4.7 9.3 - - + -
37T ARG* 4.5 11.5 - - - +
114T VAL 3.2 5.4 - - - +
115T ASN* 3.2 31.4 + - - +
202T SO4 4.1 15.2 + - - -
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Residues in contact with ALA 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15T HIS* 4.1 4.9 - - + -
16T ARG* 1.3 75.8 - - - +
18T GLN* 1.3 61.2 + - - +
19T VAL* 5.7 0.5 - - - +
30T HIS* 5.0 4.3 - - + -
31T ASP 3.6 5.2 - - - -
32T TRP* 4.1 2.5 - - + -
105T PHE 4.1 3.1 - - - +
106T LEU* 3.6 32.1 - - + -
107T HIS* 5.3 1.4 + - - +
113T PRO* 3.5 5.0 - - - +
114T VAL* 2.9 54.7 + - + +
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Residues in contact with GLN 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T ARG* 4.2 0.4 - - + -
17T ALA* 1.3 73.9 - - - +
19T VAL* 1.3 75.3 + - - +
21T LYS* 5.6 10.5 - - - +
30T HIS* 3.4 6.4 - - - +
31T ASP* 2.8 39.6 + - + +
113T PRO* 4.2 23.3 - - + +
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Residues in contact with VAL 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17T ALA 5.7 0.2 - - - +
18T GLN* 1.3 89.0 + - - +
20T ARG* 1.3 76.7 + - - +
21T LYS* 5.1 2.1 - - - +
29T THR* 3.9 13.2 - - - +
30T HIS* 3.4 28.3 - - + +
31T ASP* 6.0 0.2 - - - -
107T HIS 4.0 8.3 - - - +
108T LEU 4.2 2.9 - - - +
109T GLU* 4.1 42.4 - - + +
111T HIS 5.5 2.7 - - - +
113T PRO* 5.5 2.1 - - + +
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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