Contacts of the strand formed by residues 57 - 67 (chain T) in PDB entry 2A3W
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 ARG 57 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53T ASN* 3.5 9.6 + - - +
54T THR* 2.9 47.2 + - - +
55T GLN 4.2 7.6 - - - -
56T GLY* 1.3 83.5 - - - +
58T ASP* 1.3 62.3 + - - +
60T GLU* 3.5 15.7 + - - +
77T ARG* 3.6 26.2 - - - +
123T TYR* 2.9 32.7 + - - -
124T PHE 5.0 0.6 + - - -
126T GLU* 3.6 27.4 + - - +
139T SER 6.4 0.2 - - - -
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Residues in contact with ASP 58 (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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347L CPJ 3.3 7.1 - - - +
53T ASN* 3.1 10.0 + - - +
56T GLY 4.2 0.6 - - - -
57T ARG* 1.3 71.8 - - - +
59T ASN* 1.3 72.6 + - - +
77T ARG* 2.8 43.0 + - + +
137T GLN 2.8 10.7 - - - +
138T ASP* 3.3 20.3 - - - +
339T CA 2.4 31.0 - - - -
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Residues in contact with ASN 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347L CPJ 3.0 39.1 + - - +
52T TYR 4.4 0.9 - - - -
53T ASN* 2.9 14.8 + - - -
58T ASP* 1.3 78.6 + - - +
60T GLU* 1.3 62.2 + - - +
61T LEU* 3.3 3.8 + - - +
62T LEU* 3.8 23.2 - - + +
74T TYR* 3.9 21.0 - - + +
76T GLY 3.6 0.7 + - - -
77T ARG* 3.0 25.6 + - - +
136T GLU* 2.9 9.0 - - - +
339T CA 2.4 26.6 - - - -
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Residues in contact with GLU 60 (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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52T TYR* 3.2 22.8 + - + +
53T ASN* 3.8 0.2 + - - -
54T THR* 3.8 32.3 - - + +
57T ARG* 3.5 14.7 + - - +
58T ASP 3.2 2.0 + - - -
59T ASN* 1.3 75.6 - - - +
61T LEU* 1.3 60.7 + - - +
75T ILE* 3.4 7.1 - - - +
76T GLY* 2.7 22.3 + - - +
77T ARG* 3.1 23.0 + - - +
123T TYR* 2.6 36.5 + - - -
125T VAL* 3.4 4.6 - - + +
126T GLU* 2.9 28.3 + - - +
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Residues in contact with LEU 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T LEU* 4.8 0.9 - - + -
33T PHE* 3.6 44.6 - - + -
35T LEU* 5.4 0.4 - - + -
50T PHE* 4.0 14.3 - - + +
52T TYR* 2.9 66.0 + - + +
60T GLU* 1.3 77.5 - - - +
62T LEU* 1.3 66.9 + - - +
63T VAL* 4.8 3.8 - - + -
73T LEU* 3.9 12.3 - - + -
74T TYR 3.2 5.4 - - - +
75T ILE* 4.4 3.1 - - + -
125T VAL* 4.4 12.3 - - + -
159T MET* 3.8 25.1 - - + -
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Residues in contact with LEU 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347L CPJ 3.5 32.1 - - + -
48T SER* 3.3 22.4 - - - +
50T PHE 3.3 16.8 - - - +
51T SER* 3.9 9.0 - - - -
52T TYR 5.2 0.4 - - - +
59T ASN* 3.8 16.4 - - + +
61T LEU* 1.3 77.1 - - - +
63T VAL* 1.3 67.1 + - - +
64T TYR* 4.1 8.5 - - + -
72T SER 3.6 1.2 - - - +
73T LEU* 3.3 7.2 - - - +
74T TYR* 2.8 60.5 + - + -
136T GLU* 3.6 20.0 - - + +
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Residues in contact with VAL 63 (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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35T LEU* 3.8 28.7 - - + -
37T PHE* 4.2 19.3 - - + -
48T SER 3.9 0.3 - - - -
49T LEU* 2.9 38.1 + - + -
50T PHE* 2.9 23.6 + - + +
61T LEU* 4.8 1.6 - - + -
62T LEU* 1.3 77.1 - - - +
64T TYR* 1.3 62.1 + - - +
71T TYR* 5.3 2.2 - - + -
72T SER 3.5 8.5 - - - +
73T LEU* 4.3 8.7 - - + -
94T ILE* 5.0 1.8 - - + -
96T VAL* 3.8 15.5 - - + -
107T PHE* 4.1 18.8 - - + -
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Residues in contact with TYR 64 (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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347L CPJ 4.1 22.9 + - + -
46T ALA* 3.3 32.7 - - + +
47T TYR 3.7 21.8 - - - -
48T SER* 3.9 12.1 - - - -
49T LEU* 5.1 2.5 - - - -
62T LEU* 3.9 6.9 - - + -
63T VAL* 1.3 76.0 - - - +
65T LYS* 1.3 61.8 + - - +
66T GLU* 3.7 30.7 + - - -
71T TYR* 3.9 0.9 - - - -
72T SER* 2.9 36.0 + - - +
74T TYR* 3.9 25.4 - + + -
136T GLU* 4.4 2.2 - - + -
148T GLN* 2.9 42.2 + - + +
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Residues in contact with LYS 65 (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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43T LEU 5.4 2.2 + - - -
45T ARG 4.4 1.1 - - - +
46T ALA* 3.2 2.6 - - - +
47T TYR* 2.8 79.9 + - + +
49T LEU* 4.1 9.1 - - + +
64T TYR* 1.3 71.2 - - - +
66T GLU* 1.3 62.4 + - - +
67T ARG* 3.5 23.1 - - - +
68T VAL* 4.0 13.7 - - - +
69T GLY 4.1 1.6 - - - +
70T GLU 3.9 4.9 - - - +
71T TYR* 3.5 38.6 + - + +
86T GLU* 3.2 27.8 + - - -
88T PHE* 5.6 3.6 - - - -
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Residues in contact with GLU 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347L CPJ 6.1 0.5 - - - +
44T SER 4.7 0.3 - - - +
45T ARG* 4.3 0.9 - - - -
46T ALA* 3.5 28.3 + - - +
64T TYR* 3.9 16.0 - - + +
65T LYS* 1.3 72.1 - - - +
67T ARG* 1.3 87.5 + - + +
70T GLU* 3.7 16.9 + - + +
72T SER* 2.8 34.5 + - - +
74T TYR* 3.8 6.4 + - - -
79T LYS* 2.8 30.3 + - - -
81T THR* 4.8 2.2 - - + +
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Residues in contact with ARG 67 (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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44T SER 4.4 11.7 - - - +
45T ARG 5.4 0.9 - - - -
65T LYS* 3.4 13.3 - - - -
66T GLU* 1.3 90.9 + - - +
68T VAL* 1.3 72.4 + - - +
69T GLY 3.3 0.5 + - - -
70T GLU* 3.1 66.4 + - + +
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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