Contacts of the strand formed by residues 94 - 103 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88G LEU* 4.0 6.4 - - - +
91G GLU* 3.2 67.2 + - + +
92G ALA 4.3 2.0 - - - +
93G GLY* 1.3 83.1 + - - +
95G VAL* 1.3 70.8 + - - +
96G TYR* 4.1 14.4 + - + -
113G TRP* 3.6 43.9 - - + -
114G ILE 3.4 17.3 - - - +
115G ASP* 3.7 7.4 - - - +
116G LEU* 3.4 9.6 - - - +
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Residues in contact with VAL 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G PHE* 4.4 8.5 - - + -
48G CYS* 4.5 5.8 - - + -
86G VAL* 5.4 1.6 - - + -
87G ASP 3.3 9.9 - - - +
88G LEU* 3.2 40.4 - - + -
94G LYS* 1.3 83.2 - - - +
96G TYR* 1.3 65.6 + - - +
97G LEU* 3.8 27.6 + - + +
113G TRP* 3.3 2.1 - - - -
114G ILE 3.1 26.1 + - - +
116G LEU* 3.5 28.0 - - + -
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Residues in contact with TYR 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G GLU 5.4 0.5 - - - +
85G TYR 3.7 1.4 - - - +
86G VAL* 3.6 3.8 - - - -
87G ASP* 2.8 45.5 + - + +
90G ARG* 3.1 62.8 + - + +
91G GLU* 3.5 42.4 + - + -
94G LYS* 4.1 12.8 + - + +
95G VAL* 1.3 77.4 - - - +
97G LEU* 1.3 60.1 + - - +
112G GLY 3.5 8.1 - - - +
113G TRP* 3.7 33.8 + + + -
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Residues in contact with LEU 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G PHE* 4.3 0.9 - - + -
48G CYS* 3.9 22.2 - - - -
53G SER* 5.4 0.7 - - - -
55G ILE* 5.5 0.4 - - + -
68G PHE* 3.5 49.1 - - + -
85G TYR 3.2 10.1 - - - +
86G VAL* 4.1 15.9 - - + -
95G VAL* 4.1 18.2 - - + +
96G TYR* 1.3 76.4 - - - +
98G LYS* 1.3 61.2 + - - +
110G TRP* 4.1 9.6 - - + -
111G LYS* 3.4 3.5 - - - +
112G GLY 2.7 37.9 + - - +
114G ILE* 3.9 28.3 - - + -
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Residues in contact with LYS 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G PHE* 3.3 14.8 - - - -
84G GLU* 3.2 33.3 + - + +
85G TYR* 2.9 56.3 + - + +
97G LEU* 1.3 76.6 - - - +
99G ALA* 1.3 63.4 + - - +
109G ILE* 3.7 30.7 - - + +
110G TRP 3.0 4.9 - - - +
111G LYS* 3.6 33.4 - - + +
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Residues in contact with ALA 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G LEU* 3.6 28.3 - - + -
67G GLN 3.6 13.9 - - - +
68G PHE* 3.5 20.4 - - + -
98G LYS* 1.3 76.6 - - - +
100G PRO* 1.3 65.5 - - - +
101G MET* 3.6 3.5 - - - +
109G ILE* 4.4 1.1 - - - -
110G TRP* 2.6 42.9 + - + +
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Residues in contact with PRO 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F PRO* 4.6 8.5 - - + -
157F PRO* 4.0 12.9 - - + +
67G GLN* 3.7 10.2 + - - +
69G PHE 3.1 29.2 - - - +
70G PRO 3.3 15.9 - - - +
85G TYR* 4.5 8.5 - - + +
98G LYS 4.3 3.1 - - - +
99G ALA* 1.3 87.8 - - - +
101G MET* 1.3 66.4 + - - +
108G VAL 3.4 11.9 - - - +
109G ILE* 4.0 17.5 - - + -
128G ASP* 4.3 7.2 - - - +
131G ARG* 4.5 8.5 - - - -
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Residues in contact with MET 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F PRO* 4.3 7.7 - - - +
157F PRO* 3.5 19.7 - - + +
159F VAL* 3.8 25.4 - - + -
64G LEU* 4.1 16.8 - - + -
65G SER 5.1 2.0 - - - +
66G LEU* 3.6 26.2 - - + -
99G ALA 3.6 20.4 - - - +
100G PRO* 1.3 77.2 - - - +
102G ILE* 1.3 67.6 + - - +
103G LEU* 4.0 20.0 - - + +
107G CYS* 3.7 3.5 - - - +
108G VAL* 3.0 34.2 + - + +
109G ILE 5.2 0.7 - - - -
110G TRP* 3.7 12.8 - - + +
125G LEU* 4.6 9.2 - - + -
131G ARG* 4.9 3.2 + - - +
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Residues in contact with ILE 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F PRO* 4.5 4.3 - - + -
157F PRO 3.2 12.7 + - - +
158F GLN* 3.9 14.9 - - + +
159F VAL 3.0 27.4 + - - +
3G ARG* 3.5 61.0 - - - +
4G VAL* 3.6 15.3 - - + -
101G MET* 1.3 80.9 - - - +
103G LEU* 1.3 58.8 + - - +
104G ASN 3.5 0.3 + - - -
105G GLY* 3.8 2.8 + - - +
106G VAL 3.2 17.9 - - - +
107G CYS* 4.1 10.1 - - - +
131G ARG* 4.3 6.1 - - - +
135G GLU* 3.8 12.3 - - - +
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Residues in contact with LEU 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F VAL* 3.3 34.1 - - + +
161F THR* 4.6 6.1 - - - +
17G PHE* 3.8 35.2 - - + -
18G PHE* 3.1 22.7 - - + -
21G LEU* 5.2 0.7 - - + -
62G THR* 5.9 0.9 - - + -
64G LEU* 4.2 16.2 - - + -
101G MET* 3.8 10.9 - - + +
102G ILE* 1.3 71.0 - - - +
104G ASN* 1.3 72.2 + - - +
106G VAL* 2.8 20.9 + - - +
108G VAL* 4.7 5.6 - - + +
125G LEU* 3.6 36.8 - - + -
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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