Contacts of the strand formed by residues 50 - 57 (chain A) in PDB entry 1WFN
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 GLY 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.5 2.8 - - - +
49A THR* 1.3 81.5 + - - +
51A TYR* 1.3 67.4 + - - -
69A LEU 3.0 13.7 - - - -
70A PRO 3.4 11.7 - - - -
71A ASN* 3.5 2.1 - - - +
93A ALA* 3.5 1.2 - - - +
94A MET* 2.5 42.9 + - - +
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Residues in contact with TYR 51 (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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21A VAL* 3.5 21.8 - - + -
38A TRP* 3.7 22.4 - - + -
40A GLU* 2.8 20.8 - - - +
41A PRO* 3.5 2.4 - - + +
48A LEU* 2.7 29.6 - - + +
50A GLY* 1.3 75.4 - - - -
52A ARG* 1.3 61.5 + - - +
53A ILE 3.8 2.3 + - - -
68A TYR* 3.8 0.7 - - - -
69A LEU* 2.7 38.5 + - + +
70A PRO 3.3 12.1 - - - +
71A ASN* 3.9 17.3 - - - -
73A THR 3.2 18.4 - - - +
74A LEU* 3.2 22.6 - - + +
92A ALA 3.1 19.3 - - - +
93A ALA* 3.4 25.6 - - + +
94A MET* 3.5 4.6 - - - +
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Residues in contact with ARG 52 (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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51A TYR* 1.3 71.8 - - - +
53A ILE* 1.3 59.8 + - - +
54A SER* 4.1 14.0 + - - +
66A THR* 3.9 20.6 - - - +
67A HIS 3.7 6.5 - - - +
68A TYR* 3.4 34.6 + - + -
90A GLU 3.7 2.1 - - - +
91A VAL* 3.6 0.6 - - - -
92A ALA* 2.5 41.9 + - + +
94A MET* 4.0 15.0 - - + +
99A GLN* 2.7 62.4 - - - +
102A VAL* 4.4 0.7 - - - +
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Residues in contact with ILE 53 (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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36A VAL* 3.7 17.9 - - + -
38A TRP* 3.5 36.3 - - + -
51A TYR 3.8 0.8 + - - -
52A ARG* 1.3 73.6 - - - +
54A SER* 1.3 72.4 + - - +
55A TRP* 5.0 5.4 - - + +
65A VAL* 5.2 0.2 - - - +
66A THR* 4.0 0.5 - - - -
67A HIS* 3.1 52.2 + - + +
69A LEU* 3.9 18.6 - - + -
76A TYR* 4.0 22.7 - - + -
78A VAL* 4.8 2.9 - - + -
89A ILE* 4.1 10.1 - - + -
90A GLU 3.2 8.3 - - - +
91A VAL* 3.7 8.5 - - + +
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Residues in contact with SER 54 (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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52A ARG* 4.1 14.6 + - - +
53A ILE* 1.3 80.2 + - - +
55A TRP* 1.3 56.2 + - - +
64A ARG* 3.6 22.3 + - - -
65A VAL* 3.1 22.2 - - - -
66A THR* 4.9 2.2 + - - -
89A ILE* 4.5 1.6 - - - -
90A GLU* 2.4 67.3 + - - +
102A VAL* 5.5 2.1 - - - +
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Residues in contact with TRP 55 (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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53A ILE* 5.0 7.9 - - + -
54A SER* 1.3 75.7 - - - +
56A GLU* 1.3 65.3 + - - +
63A THR 4.4 7.3 + - - -
64A ARG* 3.2 1.6 - - - +
65A VAL* 2.8 48.2 + - + +
67A HIS* 3.2 33.9 - + + -
76A TYR* 3.2 31.4 - + - -
78A VAL* 3.1 40.2 - - + +
79A THR* 3.8 23.5 + - - -
80A GLY 5.4 2.2 + - - -
81A LEU* 3.8 12.2 - - + +
87A TYR* 5.6 0.4 - + - -
88A THR 3.6 4.0 - - - -
89A ILE* 3.2 27.6 - - + -
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Residues in contact with GLU 56 (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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55A TRP* 1.3 80.0 - - - +
57A GLU* 1.3 74.3 + - - +
58A TYR 4.8 2.9 - - - +
59A ASN* 5.1 0.7 - - - -
60A ARG 3.8 7.0 + - - +
61A THR* 2.8 35.7 + - - +
63A THR 3.4 8.1 - - - +
64A ARG* 3.2 34.9 + - + +
87A TYR* 3.5 6.9 - - - -
88A THR* 2.5 46.7 + - + +
89A ILE* 4.1 0.8 - - - +
90A GLU* 3.2 24.0 - - - +
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Residues in contact with GLU 57 (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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56A GLU* 1.3 99.2 - - - +
58A TYR* 1.3 71.8 + - - +
59A ASN* 3.4 2.6 + - - +
60A ARG* 3.5 41.7 + - + +
63A THR* 3.3 17.3 + - + +
82A THR* 4.6 4.3 + - - +
85A THR* 2.9 28.1 - - - +
86A THR 3.4 7.4 + - - +
87A TYR* 3.2 39.1 + - + +
88A THR* 3.7 2.6 + - - -
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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