Contacts of the strand formed by residues 31 - 38 (chain A) in PDB entry 3IVV
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 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.5 10.6 - - - +
30A VAL* 1.3 95.8 - - + +
32A PHE* 1.3 66.9 + - - +
161A VAL 3.2 8.1 - - - +
162A SER* 3.4 29.3 + - - +
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Residues in contact with PHE 32 (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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29A VAL* 4.0 9.9 - - + -
30A VAL 4.2 4.9 - - - -
31A LYS* 1.3 84.3 - - - +
33A SER* 1.3 64.7 + - - +
34A TYR 5.7 0.2 - - - -
57A PHE* 3.8 21.5 - + - -
58A SER 4.8 3.8 - - - +
59A SER* 3.2 37.7 - - - -
67A TRP* 3.4 30.3 - + - -
159A CYS 3.7 1.4 - - - +
160A GLU* 3.4 2.0 - - - +
161A VAL* 2.8 66.4 + - + -
163A VAL* 3.8 15.0 - - + -
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Residues in contact with SER 33 (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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32A PHE* 1.3 76.6 - - - +
34A TYR* 1.3 59.0 + - - +
35A MET* 4.1 1.6 + - - +
158A PHE* 3.6 22.2 - - - -
159A CYS 3.3 4.9 - - - -
160A GLU* 2.5 34.4 + - - +
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Residues in contact with TYR 34 (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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32A PHE* 4.2 0.6 - - + -
33A SER* 1.3 73.6 - - - +
35A MET* 1.3 66.7 + - - +
36A TRP* 3.7 28.4 - - + -
54A SER* 3.3 28.9 - - - -
55A SER* 2.7 29.2 + - - -
57A PHE* 3.3 62.8 - + + -
69A LEU* 3.7 17.7 - - + -
157A LEU 3.8 1.0 - - - +
158A PHE* 3.4 5.0 - - - -
159A CYS* 2.8 42.9 + - + +
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Residues in contact with MET 35 (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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33A SER 4.1 1.6 + - - +
34A TYR* 1.3 82.9 - - - +
36A TRP* 1.3 62.9 + - - +
37A THR* 5.1 2.2 - - - +
107A LEU* 3.5 27.6 - - + -
156A THR* 3.7 20.9 - - + -
157A LEU 3.4 4.5 - - - +
158A PHE* 3.9 20.0 - - + -
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Residues in contact with TRP 36 (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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34A TYR* 3.7 22.9 - + + -
35A MET* 1.3 76.4 - - - +
37A THR* 1.3 76.0 + - - +
38A ILE* 3.8 19.5 - - + +
52A ILE* 3.7 37.2 - - + -
53A LYS 4.0 1.8 - - - -
54A SER* 3.6 41.4 - - - +
55A SER 5.4 0.4 - - - +
69A LEU* 4.0 29.4 - - + -
71A VAL* 3.9 15.3 - - + -
155A LEU 3.5 2.1 - - - +
156A THR* 3.4 1.4 - - - -
157A LEU* 2.8 54.4 + - + +
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Residues in contact with THR 37 (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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35A MET* 4.3 3.8 - - - +
36A TRP* 1.3 82.5 + - - +
38A ILE* 1.3 63.9 + - - +
39A ASN* 3.9 19.6 + - - +
154A LYS* 3.8 29.8 - - + -
155A LEU 3.3 3.6 - - - +
156A THR* 2.8 30.8 + - - +
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Residues in contact with ILE 38 (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 TRP* 3.8 45.3 - - + +
37A THR* 1.3 74.6 - - - +
39A ASN* 1.3 72.9 + - - +
41A PHE* 4.1 18.7 - - + +
44A CYS* 4.4 11.0 - - - -
52A ILE* 4.5 13.2 - - + -
71A VAL* 3.9 18.2 - - + -
153A ASP 4.0 0.5 - - - +
154A LYS* 3.5 1.7 - - - -
155A LEU* 2.8 51.7 + - + +
157A LEU* 4.5 10.5 - - + -
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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