Contacts of the strand formed by residues 45 - 54 (chain F) in PDB entry 3ZWG
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 TRP 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F ILE* 3.5 24.2 - - + -
38F ASP 3.7 2.7 - - - -
39F ASN* 2.9 39.7 - - + -
41F SER* 2.9 20.2 + - - -
43F LYS 3.6 7.4 - - - -
44F THR* 1.3 77.0 - - - +
46F THR* 1.3 65.3 + - - +
64F LYS* 3.6 6.8 - - - +
65F VAL* 2.8 49.5 + - + +
71F LEU* 4.4 11.0 - - + -
92F TYR* 3.9 20.8 - + + -
93F SER 3.3 5.6 - - - +
94F MET* 3.7 25.2 - - + +
100F LEU* 3.5 30.1 - - + -
176F VAL* 3.6 34.1 - - + -
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Residues in contact with THR 46 (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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44F THR* 4.3 5.4 + - - +
45F TRP* 1.3 77.0 - - - +
47F ALA* 1.3 66.5 + - - +
63F HIS* 3.2 33.0 - - + +
64F LYS* 3.0 32.9 + - - +
92F TYR* 3.4 4.0 - - - -
93F SER* 2.7 53.3 + - - -
94F MET 5.9 0.2 - - - -
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Residues in contact with ALA 47 (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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149E TRP* 3.6 24.6 - - + +
46F THR* 1.3 75.2 - - - +
48F MET* 1.3 60.3 + - - +
61F LEU* 3.6 24.7 - - + +
62F PRO 3.5 12.1 - - - +
63F HIS* 2.9 22.8 + - - +
91F ALA 4.2 0.2 - - - -
92F TYR* 3.3 26.3 - - + -
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Residues in contact with MET 48 (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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149E TRP* 2.7 39.2 + - - +
46F THR 3.5 0.2 + - - -
47F ALA* 1.3 75.7 - - - +
49F ASN* 1.3 66.0 + - - +
61F LEU* 4.5 0.2 - - - -
91F ALA* 2.9 16.6 + - + +
92F TYR 3.7 5.8 - - - -
93F SER* 3.5 34.8 - - - +
99F THR* 3.5 20.6 - - + +
125F GLN* 4.3 16.8 - - - +
126F LYS 3.4 32.1 - - - +
127F ARG* 3.8 23.4 + - + +
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Residues in contact with ASN 49 (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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146E ASP* 4.9 5.5 + - - -
147E ASN 3.6 4.3 - - - +
148E GLY* 3.2 19.1 - - - -
48F MET* 1.3 85.5 - - - +
50F THR* 1.3 80.4 + - - +
51F TYR* 3.8 1.6 - - - +
61F LEU* 3.7 10.9 - - - +
89F VAL 3.8 0.9 - - - +
90F ILE* 3.6 1.0 - - - -
91F ALA* 2.8 30.9 + - - +
127F ARG* 3.6 24.5 - - - +
128F ALA* 3.0 43.1 + - - +
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Residues in contact with THR 50 (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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146E ASP 3.6 17.0 - - - +
147E ASN* 3.1 13.4 + - - +
49F ASN* 1.3 85.0 + - - +
51F TYR* 1.3 66.9 + - - +
52F PHE* 3.4 36.6 + - + -
61F LEU* 3.8 11.6 - - - +
73F TYR* 3.1 30.6 + - + +
89F VAL 3.2 16.4 - - - +
90F ILE* 3.9 9.8 - - + +
104F PHE* 4.5 2.7 - - + -
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Residues in contact with TYR 51 (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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49F ASN* 3.8 3.0 - - - +
50F THR* 1.3 74.6 - - - +
52F PHE* 1.3 69.8 + - - +
53F ARG* 4.0 21.1 - - + -
88F GLY* 3.1 5.9 - - - -
89F VAL* 2.8 37.2 + - + +
128F ALA* 3.6 26.9 - - + +
129F ASP* 3.7 20.6 - - - +
130F GLN* 2.7 52.3 + - + +
133F TYR* 4.1 15.3 - - + -
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Residues in contact with PHE 52 (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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147E ASN* 4.1 21.3 - - + -
166E SER* 5.8 0.2 - - - -
50F THR* 3.4 26.3 + - + -
51F TYR* 1.3 82.9 - - - +
53F ARG* 1.3 65.2 + - - +
54F SER 3.7 16.8 - - - +
55F GLY 3.2 25.6 - - - +
56F THR* 3.8 11.2 - - - -
57F SER* 3.6 31.4 - - - -
73F TYR* 3.9 17.5 - + - -
75F GLY* 4.6 3.4 - - - -
86F VAL* 4.1 10.3 - - + -
87F VAL 3.6 5.2 - - - -
104F PHE* 3.9 20.6 - + - -
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Residues in contact with ARG 53 (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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51F TYR* 3.6 22.9 + - + -
52F PHE* 1.3 73.9 - - - +
54F SER* 1.3 70.6 + - - +
87F VAL* 2.7 26.3 + - + +
88F GLY* 5.1 0.2 - - - -
130F GLN* 3.4 31.8 + - - +
133F TYR* 3.8 31.2 + - + +
138F TYR* 5.5 3.8 + - - -
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Residues in contact with SER 54 (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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52F PHE* 3.7 6.0 - - - -
53F ARG* 1.3 94.7 + - - +
55F GLY* 1.3 63.4 + - - +
78F ASN* 4.4 2.0 - - - -
84F THR* 4.4 17.1 - - - +
85F GLY 3.4 22.8 + - - -
86F VAL* 3.3 2.1 - - - -
87F VAL* 2.9 36.5 + - - +
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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