Contacts of the strand formed by residues 57 - 67 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53L ASN* 3.6 7.4 - - - +
54L THR* 2.8 46.2 + - - +
55L GLN 3.7 8.7 - - - +
56L GLY* 1.3 84.5 - - - +
58L ASP* 1.3 65.6 + - - +
60L GLU* 2.8 29.7 + - - +
76L GLY* 4.4 1.0 - - - -
77L ARG* 3.6 36.3 - - - +
120L ARG* 4.1 4.0 - - - +
123L TYR* 2.8 34.1 + - - -
126L GLU* 4.4 14.3 - - - +
139L SER 6.4 0.7 - - - -
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Residues in contact with ASP 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L ASN* 3.0 12.3 + - - +
56L GLY 4.2 1.0 - - - -
57L ARG* 1.3 73.8 - - - +
59L ASN* 1.3 81.0 + - - +
60L GLU* 3.1 2.5 + - - +
76L GLY 4.9 0.2 - - - -
77L ARG* 3.3 25.7 - - + +
137L GLN 2.8 10.9 - - - +
138L ASP* 3.4 19.9 - - - +
324L CA 2.4 30.1 - - - -
347L CPJ 3.2 7.6 - - - +
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Residues in contact with ASN 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L TYR 4.5 0.4 - - - -
53L ASN* 2.9 13.4 + - - -
58L ASP* 1.3 78.8 + - - +
60L GLU* 1.3 63.8 + - - +
61L LEU* 3.3 4.7 + - - +
62L LEU* 4.1 12.8 - - + -
74L TYR* 3.8 29.1 - - + +
76L GLY 3.6 0.9 + - - -
77L ARG* 3.0 25.6 + - + +
136L GLU* 2.8 12.6 - - - +
324L CA 2.3 25.8 - - - -
347L CPJ 2.9 35.1 + - - +
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Residues in contact with GLU 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L TYR* 3.3 22.0 + - + +
54L THR* 4.0 20.9 - - + +
57L ARG* 2.8 41.2 + - - +
58L ASP 3.1 3.2 + - - +
59L ASN* 1.3 76.0 - - - +
61L LEU* 1.3 60.4 + - - +
74L TYR 4.1 0.2 - - - -
75L ILE* 3.3 8.3 - - - +
76L GLY* 2.9 27.3 + - - +
123L TYR* 2.4 27.3 + - - -
125L VAL* 3.3 8.0 - - + +
126L GLU* 2.9 29.2 + - - +
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Residues in contact with LEU 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L PHE* 3.5 46.7 - - + -
35L LEU* 5.5 0.7 - - + -
50L PHE* 3.9 12.6 - - + +
51L SER 3.9 0.5 - - - -
52L TYR* 2.9 64.9 + - + +
59L ASN 3.3 0.2 - - - -
60L GLU* 1.3 79.1 - - - +
62L LEU* 1.3 66.2 + - - +
63L VAL* 4.9 2.9 - - + -
73L LEU* 3.7 16.2 - - + -
74L TYR 3.3 4.5 - - - +
75L ILE* 4.3 2.5 - - + -
125L VAL* 4.5 11.4 - - + -
159L MET* 3.7 25.4 - - + -
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Residues in contact with LEU 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L SER* 3.2 28.9 - - - +
50L PHE 3.3 11.9 - - - +
51L SER* 4.0 5.6 - - - -
52L TYR 5.1 0.7 - - - +
53L ASN* 5.9 0.2 - - - +
59L ASN* 3.9 13.9 - - - +
61L LEU* 1.3 75.1 - - - +
63L VAL* 1.3 69.3 + - - +
64L TYR* 4.0 10.8 - - + -
72L SER 3.5 0.9 - - - +
73L LEU* 3.3 8.5 - - - +
74L TYR* 2.8 58.4 + - + -
136L GLU* 3.6 21.3 - - + +
347L CPJ 3.5 33.2 - - + -
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Residues in contact with VAL 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L LEU* 3.9 18.6 - - + -
37L PHE* 4.2 10.8 - - + -
49L LEU* 2.8 45.5 + - + +
50L PHE* 2.9 22.9 + - + -
61L LEU* 4.9 2.7 - - + -
62L LEU* 1.3 79.0 - - - +
64L TYR* 1.3 62.4 + - - +
65L LYS 4.3 0.2 - - - -
71L TYR* 5.3 2.9 - - + -
72L SER 3.4 7.9 - - - +
73L LEU* 4.0 9.4 - - + -
94L ILE* 5.0 2.2 - - + -
96L VAL* 3.8 26.2 - - + -
107L PHE* 4.2 17.7 - - + -
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Residues in contact with TYR 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L ALA* 3.5 24.4 - - + +
47L TYR 3.5 24.0 - - - -
48L SER* 3.9 11.9 - - - -
49L LEU* 5.2 0.2 - - - -
62L LEU* 4.0 16.4 - - + -
63L VAL* 1.3 76.9 - - - +
65L LYS* 1.3 59.6 + - - +
66L GLU* 3.7 32.0 + - + -
71L TYR* 3.7 1.7 - - - +
72L SER* 2.8 42.7 + - - +
74L TYR* 4.0 29.4 - + + -
136L GLU* 4.6 0.7 - - + -
148L GLN* 3.2 42.5 + - + +
347L CPJ 4.0 20.1 - - + -
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Residues in contact with LYS 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L LEU 5.8 1.4 + - - -
45L ARG 5.7 0.4 - - - +
46L ALA* 3.2 6.2 - - - +
47L TYR* 2.9 80.1 + - + +
49L LEU* 4.1 10.2 - - + +
63L VAL 4.3 0.4 + - - -
64L TYR* 1.3 73.5 - - - +
66L GLU* 1.3 57.6 + - - +
67L ARG* 3.6 20.0 - - - +
68L VAL* 3.9 12.9 - - - +
69L GLY 4.2 1.3 - - - +
70L GLU 3.7 11.0 - - - +
71L TYR* 3.6 30.7 + - + +
86L GLU* 2.6 31.4 + - - -
88L PHE* 5.6 4.0 - - - -
92L VAL* 6.2 0.6 - - - +
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Residues in contact with GLU 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L SER 4.9 0.5 - - - +
46L ALA* 3.4 33.0 + - - +
64L TYR* 3.7 24.5 + - + -
65L LYS* 1.3 73.0 - - - +
67L ARG* 1.3 96.3 + - - +
70L GLU* 3.6 16.1 + - + +
72L SER* 4.6 13.5 - - - +
74L TYR* 5.8 0.4 - - - +
79L LYS* 5.1 12.3 + - - -
81L THR* 5.8 0.4 - - + -
347L CPJ 5.9 2.9 - - - -
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Residues in contact with ARG 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L SER 4.5 12.3 - - - +
45L ARG 5.5 1.1 - - - -
65L LYS* 3.5 11.3 - - - -
66L GLU* 1.3 105.6 + - - +
68L VAL* 1.3 72.2 + - - +
69L GLY 3.3 0.3 + - - -
70L GLU* 2.8 71.4 + - + +
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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