Contacts of the strand formed by residues 94 - 103 (chain B) in PDB entry 3WTW
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 LYS 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 4.0 10.7 - - - +
91B GLU* 3.0 60.5 + - + +
92B ALA 3.8 0.6 - - - -
93B GLY* 1.3 80.5 + - - +
95B VAL* 1.3 69.6 - - - +
96B TYR* 4.1 15.7 - - + +
113B TRP* 3.2 47.6 - - + -
114B ILE 3.5 8.3 - - - +
115B ASP* 4.6 10.6 + - + -
116B LEU* 4.5 1.7 - - - +
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PHE* 5.1 6.5 - - + -
45B GLN* 5.7 0.2 - - + -
48B CYS* 4.8 9.4 - - + -
86B VAL* 4.4 4.9 - - + -
87B ASP 3.3 15.3 - - - +
88B LEU* 4.2 19.7 - - + +
94B LYS* 1.3 82.4 - - - +
96B TYR* 1.3 62.2 + - - +
97B LEU* 3.5 31.3 + - + +
113B TRP* 3.3 16.5 - - - -
114B ILE 3.1 14.0 + - - +
116B LEU* 3.3 40.6 - - + -
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU 5.1 0.3 - - - +
85B TYR 4.1 0.7 - - - +
86B VAL* 3.6 1.4 - - - -
87B ASP* 2.7 52.0 + - + +
88B LEU* 6.2 0.2 - - - -
90B ARG* 3.2 83.0 + - + +
91B GLU* 3.8 16.3 + - + -
94B LYS* 4.1 14.5 - - + +
95B VAL* 1.3 76.8 - - - +
97B LEU* 1.3 61.2 + - - +
112B GLY 3.5 7.6 - - - -
113B TRP* 3.9 33.8 + + + +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PHE* 4.7 2.5 - - + -
48B CYS* 4.0 14.8 - - - -
55B ILE* 4.4 19.7 - - + -
68B PHE* 3.4 40.6 - - + -
84B GLU 5.9 0.2 - - - -
85B TYR 3.4 4.0 - - - -
86B VAL* 3.5 34.8 - - + -
95B VAL* 3.9 20.0 - - + +
96B TYR* 1.3 77.7 - - - +
98B LYS* 1.3 66.6 + - - +
110B TRP* 3.9 12.3 - - + -
111B LYS* 3.8 3.3 - - - +
112B GLY 2.8 24.5 + - - +
114B ILE* 4.5 10.3 - - + -
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Residues in contact with LYS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.2 18.4 - - - -
84B GLU* 3.9 22.6 + - - +
85B TYR* 3.0 50.7 + - + +
97B LEU* 1.3 81.5 - - - +
99B ALA* 1.3 68.5 + - - +
109B ILE* 3.8 21.3 - - + +
110B TRP* 3.1 8.5 - - - -
111B LYS* 3.5 42.0 - - + +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 4.3 12.8 - - + -
67B GLN 3.0 37.0 - - - +
68B PHE* 3.6 9.9 - - + -
98B LYS* 1.3 78.9 - - - +
100B PRO* 1.3 68.5 - - - +
101B MET* 4.7 2.4 - - + +
109B ILE* 4.3 2.2 - - - -
110B TRP* 2.7 42.3 + - + +
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Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PRO* 4.5 7.9 - - + -
157A PRO* 4.1 11.0 - - + +
67B GLN 4.1 2.4 - - - +
69B PHE 3.2 28.5 - - - +
70B PRO* 4.8 0.9 - - + -
71B ALA* 4.2 25.1 - - + +
85B TYR* 4.6 10.8 - - + +
99B ALA* 1.3 91.1 - - + +
101B MET* 1.3 71.5 - - - +
108B VAL 3.2 14.4 - - - +
109B ILE* 3.9 15.9 - - + -
128B ASP* 4.2 8.3 - - - +
131B ARG* 5.2 1.1 - - + -
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Residues in contact with MET 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PRO* 4.5 8.4 - - - +
157A PRO* 3.6 24.0 - - + +
159A VAL* 4.1 18.6 - - + -
64B LEU* 4.1 22.7 - - + -
65B SER 3.5 25.1 - - - +
66B LEU* 4.0 19.7 - - + -
99B ALA* 4.7 6.3 - - + +
100B PRO* 1.3 87.2 - - - +
102B ILE* 1.3 64.8 + - - +
103B LEU* 3.8 16.8 + - + +
107B CYS* 3.4 3.8 - - - +
108B VAL* 2.9 40.6 + - + +
110B TRP* 4.8 5.8 - - - -
125B LEU* 5.3 3.6 - - - -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER* 5.5 0.9 + - - -
156A PRO* 4.4 14.6 - - + -
157A PRO 3.4 4.9 + - - -
158A GLN* 4.0 24.5 - - + +
159A VAL 3.3 17.5 + - - +
3B ARG* 3.2 50.7 - - + +
4B VAL* 3.5 24.5 - - + -
101B MET* 1.3 79.1 - - - +
103B LEU* 1.3 60.0 + - - +
104B ASN 3.4 1.2 + - - -
105B GLY* 3.9 12.3 + - - +
106B VAL 3.8 7.4 - - - +
107B CYS* 4.0 11.4 - - - -
131B ARG* 5.0 0.7 - - - +
135B GLU* 3.7 11.9 - - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A VAL* 3.2 38.3 - - + +
161A THR* 4.3 7.2 - - + -
17B PHE* 4.0 18.4 - - + -
18B PHE* 3.5 21.7 - - + -
21B LEU* 5.7 0.9 - - + -
62B THR* 6.2 0.9 - - + -
64B LEU* 4.3 19.1 - - + -
101B MET* 3.6 10.2 - - + -
102B ILE* 1.3 72.5 - - - +
104B ASN* 1.3 90.9 + - - +
106B VAL* 3.1 19.4 + - - +
108B VAL* 5.0 3.1 - - + -
125B LEU* 3.8 28.7 - - + -
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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