Contacts of the strand formed by residues 30 - 37 (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 HIS 30 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16H PRO* 5.6 9.2 - - + -
17T ALA 5.0 2.5 - - - -
18T GLN 3.4 14.4 - - - +
19T VAL* 3.4 25.8 - - + +
20T ARG* 4.0 1.1 - - - -
28T PHE* 4.7 0.3 - - - +
29T THR* 1.3 113.7 + - - +
31T ASP* 1.3 73.6 + - - +
32T TRP* 4.6 4.7 - - + -
76T SER* 3.3 3.1 - - - -
77T GLY 2.9 28.3 + - - +
78T TYR 5.0 2.7 - - - -
106T LEU* 3.6 43.3 - - + +
107T HIS 2.8 28.8 + - - -
108T LEU* 5.5 2.7 - - + -
109T GLU 5.9 0.4 - - - -
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Residues in contact with ASP 31 (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 4.6 0.5 - - - -
17T ALA* 3.6 0.7 - - - -
18T GLN* 2.8 38.3 + - + +
20T ARG* 2.8 47.9 + - + +
30T HIS* 1.3 78.9 - - - +
32T TRP* 1.3 60.5 + - - +
75T GLU 3.7 4.0 - - - +
76T SER* 2.9 15.3 + - - -
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Residues in contact with TRP 32 (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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15T HIS* 5.2 1.1 - - + -
16T ARG 3.1 14.6 - - - +
17T ALA* 4.1 11.7 - - + -
30T HIS* 4.5 5.2 - - + -
31T ASP* 1.3 77.0 - - - +
33T MET* 1.3 67.1 + - - +
34T VAL* 4.2 13.7 - - + -
55T LEU* 3.8 17.5 - - + -
59T PHE* 3.5 25.3 - + - -
73T VAL* 5.1 4.3 - - + -
74T GLU* 3.7 1.4 - - - +
75T GLU* 2.9 59.2 + - + +
76T SER 4.0 0.6 - - - -
77T GLY* 3.6 29.0 - - - +
79T ALA 5.2 3.2 + - - -
81T PHE* 3.8 25.4 - + - -
104T LEU* 3.4 37.4 - - + +
106T LEU* 4.4 16.6 - - + +
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Residues in contact with MET 33 (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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15T HIS* 3.1 5.2 - - - +
16T ARG* 2.8 76.3 + - + +
32T TRP* 1.3 77.2 - - - +
34T VAL* 1.3 64.4 + - - +
35T PHE* 3.6 24.5 - - + -
72T LYS* 4.0 23.1 - - + -
73T VAL 3.3 18.6 - - - +
74T GLU* 3.7 22.2 - - + +
202T SO4 4.1 13.5 - - - +
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Residues in contact with VAL 34 (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 3.5 12.1 - - - +
15T HIS* 3.8 7.6 - - + -
32T TRP* 4.2 10.4 - - + -
33T MET* 1.3 75.0 - - - +
35T PHE* 1.3 65.1 + - - +
53T PHE* 3.8 28.9 - - + -
72T LYS* 3.2 5.1 - - - +
73T VAL* 3.1 36.6 + - + -
83T LEU* 3.9 17.9 - - + -
85T ILE* 4.4 9.6 - - + -
102T TYR* 4.1 21.5 - - + -
104T LEU* 3.8 13.2 - - + -
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Residues in contact with PHE 35 (chain T).
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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12T GLU 4.5 3.1 - - - -
13T LEU* 3.6 2.3 - - - +
14T GLY* 2.9 55.7 + - - +
15T HIS* 3.8 7.0 - - - -
16T ARG* 4.7 10.3 - - + -
33T MET* 3.6 28.7 - - + -
34T VAL* 1.3 78.9 - - - +
36T VAL* 1.3 72.8 + - - +
37T ARG* 3.6 48.2 - - + -
53T PHE* 4.2 2.7 - - - -
71T TYR 3.2 11.2 - - - +
72T LYS* 3.6 2.7 - - + -
85T ILE* 5.2 0.2 - - - +
115T ASN* 6.0 0.2 - - - -
116T HIS 5.0 0.2 - - - -
117T LEU* 3.8 24.7 - - + -
202T SO4 3.3 23.8 - - - +
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Residues in contact with VAL 36 (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* 4.5 9.9 - - + -
12T GLU 3.4 7.6 - - - +
13T LEU* 3.9 23.3 - - + -
35T PHE* 1.3 80.6 - - - +
37T ARG* 1.3 67.7 + - - +
44T ILE* 4.4 11.9 - - + -
51T VAL* 4.2 11.2 - - + -
53T PHE* 4.1 8.5 - - + -
71T TYR* 2.8 39.0 + - + +
85T ILE* 3.9 29.6 - - + -
87T VAL* 4.5 17.3 - - + -
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Residues in contact with ARG 37 (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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115K ASN* 4.5 7.5 + - - +
11T LEU* 3.5 4.7 - - - +
12T GLU* 2.6 72.7 + - + +
16T ARG* 4.5 10.5 - - - +
35T PHE* 3.6 22.7 - - + -
36T VAL* 1.3 78.1 - - - +
38T GLY* 1.3 64.3 + - - +
44T ILE* 3.7 14.4 - - - -
117T LEU* 4.3 17.0 - - - +
202T SO4 3.5 37.9 + - - +
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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