Contacts of the strand formed by residues 60 - 67 (chain A) in PDB entry 1WFO
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ILE* 3.3 1.9 - - - +
59A LEU* 1.3 86.4 - - - +
61A TYR* 1.3 66.9 + - - +
79A VAL* 4.3 12.8 - - + -
80A LEU 2.7 21.5 - - - +
81A ALA* 4.0 2.7 - - - -
82A PRO* 3.3 12.7 - - - +
105A GLN* 2.6 46.0 + - + +
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO* 4.8 7.4 - - + -
48A TRP* 3.5 37.0 - + + -
50A PRO* 3.8 24.9 - - + +
51A PRO* 3.8 9.9 - - + +
58A ILE* 3.0 31.3 - - + +
60A ALA* 1.3 87.8 - - - +
62A GLN* 1.3 57.7 + - - +
79A VAL* 3.0 6.9 - - - -
80A LEU* 2.5 48.0 + - + +
81A ALA 3.2 17.3 - - - +
82A PRO 3.8 12.3 - - - -
84A ALA 4.2 8.3 - - - -
102A ILE* 4.1 5.4 - - + -
103A THR 2.9 22.0 - - - -
104A ALA* 3.6 11.8 - - + +
110A TRP* 3.2 12.3 - - - -
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 1.3 74.5 - - - +
63A ILE* 1.3 66.0 + - - +
64A THR* 3.5 16.3 - - + +
77A VAL* 3.1 35.9 - - + +
78A GLU 3.1 11.4 - - - +
79A VAL* 3.6 14.1 - - + +
80A LEU* 4.8 0.2 - - - -
101A ARG* 2.9 7.9 - - - +
102A ILE* 3.2 3.1 - - - +
103A THR* 2.7 37.8 + - - +
110A TRP* 3.2 32.3 + - + -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 4.9 0.7 - - + -
48A TRP* 3.0 35.2 - - + -
62A GLN* 1.3 72.9 - - - +
64A THR* 1.3 59.8 + - - +
65A HIS* 3.3 11.1 + - - +
78A GLU 2.6 28.9 + - - +
80A LEU* 3.0 30.7 - - + +
87A TYR* 3.2 48.0 - - + -
100A PHE* 4.4 15.3 - - + -
101A ARG 3.2 2.2 - - - +
102A ILE* 3.3 26.5 - - + -
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLN* 3.5 17.7 - - + +
63A ILE* 1.3 71.3 - - - +
65A HIS* 1.3 53.9 + - - +
66A ARG* 5.6 4.4 + - - -
75A ALA* 5.2 5.8 - - - -
77A VAL* 3.4 36.8 - - + -
99A LEU* 2.8 25.0 + - - +
100A PHE* 3.3 2.8 - - - -
101A ARG* 2.7 56.2 + - + +
103A THR* 5.6 2.0 - - - +
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Residues in contact with HIS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 3.3 17.9 + - - +
64A THR* 1.3 74.5 - - - +
66A ARG* 1.3 63.8 + - - +
75A ALA* 3.8 10.0 - - - +
76A THR* 2.8 42.0 + - + +
78A GLU* 4.2 8.7 - - + -
87A TYR* 3.1 28.2 + - - -
89A ALA* 4.9 4.7 - - + -
90A THR 5.6 3.6 + - - -
92A LEU* 4.5 16.4 - - + -
98A TYR* 4.5 8.2 - + + -
99A LEU 3.6 3.6 - - - -
100A PHE* 4.3 25.1 - - + -
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A THR* 5.6 4.4 + - - -
65A HIS* 1.3 76.2 - - - +
67A LEU* 1.3 69.2 + - - +
68A ASN* 5.6 5.7 + - - +
74A THR 5.5 1.1 - - - +
75A ALA* 3.4 25.1 - - + +
98A TYR* 3.1 16.8 - - - -
99A LEU* 2.9 61.3 + - + +
101A ARG* 5.2 8.3 - - - +
115A GLU* 5.1 6.0 + - - -
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ARG* 1.3 80.0 + - - +
68A ASN* 1.3 66.7 + - - +
69A THR* 3.0 5.5 + - - +
70A THR* 3.0 42.1 + - + +
93A LYS* 3.3 42.8 - - + +
96A SER* 3.3 15.3 - - - +
97A VAL 2.8 27.4 - - - +
98A TYR* 3.0 42.5 - - + +
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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