Contacts of the strand formed by residues 158 - 169 (chain F) in PDB entry 3WTV
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 GLN 158 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ASN* 3.6 20.1 + - - +
70F PHE* 3.6 31.8 - - + -
97F VAL* 4.5 6.7 - - - +
150F ILE 4.1 0.2 - - - +
151F THR* 3.5 1.4 - - - -
152F VAL* 2.7 42.9 + - - +
154F THR* 3.1 34.6 + - - +
156F PRO 4.1 2.5 - - - +
157F PRO* 1.3 75.3 - - - +
159F VAL* 1.3 61.9 + - - +
160F ALA 4.3 0.2 + - - -
3G ARG* 3.8 40.2 + - - +
102G ILE* 3.5 17.4 - - + +
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Residues in contact with VAL 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F SER* 4.2 3.6 + - - -
70F PHE* 5.8 0.2 - - - -
149F THR* 3.6 15.0 - - + -
150F ILE 3.4 9.9 - - - +
151F THR* 3.9 17.7 - - + +
157F PRO* 4.9 2.7 - - + -
158F GLN* 1.3 79.5 - - - +
160F ALA* 1.3 67.9 + - - +
161F THR* 5.1 0.9 - - - +
64G LEU* 3.5 26.0 - - + -
65G SER 5.3 3.8 - - - +
101G MET* 3.8 28.0 - - + -
102G ILE 2.8 14.1 + - - +
103G LEU* 4.3 15.0 - - + -
104G ASN* 2.9 26.6 + - - -
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Residues in contact with ALA 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F THR* 3.6 18.4 - - + +
67F SER* 3.3 26.0 - - - -
70F PHE* 4.4 12.3 - - + -
149F THR* 3.7 1.4 - - - -
150F ILE* 2.7 51.4 + - + +
152F VAL* 6.5 0.2 - - + -
158F GLN 4.3 0.4 + - - -
159F VAL* 1.3 75.2 - - - +
161F THR* 1.3 62.1 + - - +
104G ASN* 3.4 4.7 - - - -
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Residues in contact with THR 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F THR* 3.7 4.1 - - - -
66F ASP* 2.7 44.4 + - - +
147F THR* 3.3 29.4 - - + -
148F LEU 3.3 6.9 + - - +
149F THR* 4.7 4.9 - - - +
150F ILE* 5.8 0.2 - - - -
159F VAL* 5.1 2.4 - - - +
160F ALA* 1.3 74.4 - - - +
162F TYR* 1.3 72.6 + - - +
163F HIS* 3.4 15.0 - - + +
17G PHE* 3.7 15.4 - - + -
62G THR* 5.8 2.2 - - + +
103G LEU* 4.1 4.3 - - - +
104G ASN* 2.8 24.8 + - - -
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Residues in contact with TYR 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F VAL* 3.7 28.4 - - + +
64F ARG 5.4 5.8 - - - -
65F THR* 5.4 2.5 - - + +
66F ASP* 3.9 1.3 - - - -
72F CYS* 3.5 30.1 - - - -
73F SER 3.8 7.0 - - - -
74F VAL* 3.8 8.5 - - - +
75F LEU* 3.6 30.3 + - + -
147F THR* 3.4 1.6 - - - -
148F LEU* 2.9 49.6 + - + -
150F ILE* 5.1 5.2 - - + -
161F THR* 1.3 78.3 - - - +
163F HIS* 1.3 74.4 + - - +
164F ARG 4.8 1.3 - - - -
165F ALA* 3.6 30.0 + - + +
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Residues in contact with HIS 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ASP* 3.1 27.2 + - - +
147F THR* 3.5 24.4 - - + +
161F THR* 3.4 21.1 - - + +
162F TYR* 1.3 81.6 - - - +
164F ARG* 1.3 92.7 + - + +
165F ALA 3.2 0.2 + - - -
17G PHE* 3.8 34.0 - + + +
62G THR* 5.8 0.8 + - - -
104G ASN* 5.2 0.9 - - - -
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Residues in contact with ARG 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F SER* 3.1 23.8 - - - +
146F PHE 3.7 5.1 + - - -
147F THR* 3.9 4.8 + - - -
162F TYR* 4.8 1.6 - - - -
163F HIS* 1.3 88.9 + - + +
165F ALA* 1.3 62.6 + - - +
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Residues in contact with ALA 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F LEU* 3.9 17.0 - - + +
76F PRO 3.6 8.8 - - - +
77F THR* 4.5 3.2 - - - -
146F PHE 3.0 9.5 + - - +
148F LEU* 4.0 14.4 - - + -
162F TYR* 3.6 50.2 + - + +
163F HIS 4.0 1.1 - - - -
164F ARG* 1.3 79.5 - - - +
166F ILE* 1.3 67.4 + - + +
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Residues in contact with ILE 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F LEU* 4.2 11.4 - - + -
76F PRO* 3.2 27.4 - - + +
77F THR 3.6 5.8 - - - +
79F TRP* 3.6 19.3 - - + -
85F LEU* 4.3 4.5 - - + -
136F PHE* 3.8 40.2 - - + -
145F SER* 3.8 6.2 - - - -
146F PHE* 2.8 37.5 + - + +
148F LEU* 5.2 0.4 - - + -
164F ARG 3.7 1.2 - - - -
165F ALA* 1.3 85.6 - - + +
167F LYS* 1.3 65.8 + - - +
168F ILE* 3.5 26.8 + - + -
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Residues in contact with LYS 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F THR 2.7 17.8 + - - +
78F HIS* 3.4 29.8 + - + +
79F TRP 2.8 28.4 + - - +
140F SER* 3.6 6.7 - - - +
141F GLY 4.4 0.9 - - - +
143F GLY* 4.2 13.9 - - - +
144F LYS 3.3 23.1 - - - +
145F SER* 4.1 4.2 - - - -
166F ILE* 1.3 72.6 - - - +
168F ILE* 1.3 66.2 + - - +
169F THR* 3.9 8.3 - - + -
3I A 4.5 2.4 + - - -
4I G 3.1 40.8 + - - +
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Residues in contact with ILE 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F TRP* 3.3 10.8 - - + +
80F ARG 5.1 2.0 - - - +
81F CYS* 3.4 31.2 - - + +
136F PHE* 3.6 25.4 - - + -
138F GLY 3.2 23.1 - - - +
139F ARG* 3.5 5.4 - - - +
140F SER* 3.1 24.9 + - - -
141F GLY 4.4 0.9 + - - -
146F PHE* 3.7 28.7 - - + -
166F ILE* 3.5 33.2 - - + +
167F LYS* 1.3 75.4 - - - +
169F THR* 1.3 71.8 + - - +
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Residues in contact with THR 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F HIS* 2.8 32.7 + - - +
79F TRP 3.4 3.6 + - - -
80F ARG* 3.6 2.6 - - - -
81F CYS* 3.1 21.0 + - - -
139F ARG* 4.2 11.0 - - + -
140F SER* 5.2 0.4 - - - +
141F GLY 5.3 5.6 - - - +
167F LYS* 3.9 13.0 - - + -
168F ILE* 1.3 81.2 - - - +
170F GLY* 1.3 65.3 + - - +
171F ASP* 3.3 1.7 + - - +
172F GLY 2.9 13.9 + - - -
4I G 3.8 27.1 - - - +
5I C 3.5 12.1 - - - +
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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