Contacts of the strand formed by residues 31 - 38 (chain A) in PDB entry 3T5D
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 GLU 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A PHE* 1.3 84.9 + - - +
32A PHE* 1.3 65.6 + - - +
33A THR* 5.9 0.9 - - - +
89A LEU* 3.2 27.4 - - + +
136A ASP* 4.0 29.4 - - - +
140A GLN* 5.8 0.2 - - - +
279A LYS* 2.8 52.3 + - - +
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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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30A PHE* 4.2 7.4 - + + -
31A GLU* 1.3 78.7 - - - +
33A THR* 1.3 70.5 + - - +
34A LEU* 3.7 33.0 - - + -
88A LEU* 5.3 1.1 - - + -
89A LEU* 2.8 12.0 + - - +
90A LEU* 3.4 16.9 - - + +
91A THR* 3.0 26.7 + - - +
140A GLN* 3.5 26.9 - - + -
141A CYS* 3.7 23.6 - - + -
270A LEU* 4.7 1.8 - - + -
275A MET* 3.6 66.2 - - + -
278A LEU* 4.4 7.9 - - + -
279A LYS* 5.3 1.8 - - + -
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Residues in contact with THR 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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31A GLU* 5.9 0.9 - - - +
32A PHE* 1.3 78.2 - - - +
34A LEU* 1.3 60.9 + - - +
76A GLN* 5.9 0.4 - - - +
91A THR* 3.1 26.9 + - - +
93A VAL* 3.8 13.0 - - + -
114A TYR* 5.4 1.6 - - - +
136A ASP 4.4 6.6 + - - -
137A ASN* 4.2 15.7 + - - +
138A ARG 3.3 22.7 + - - +
139A VAL* 3.7 24.9 - - + -
140A GLN* 2.7 29.4 + - - +
141A CYS 3.3 8.7 + - - +
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Residues in contact with LEU 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* 3.7 23.9 + - + -
33A THR* 1.3 73.0 - - - +
35A MET* 1.3 59.9 + - - +
36A VAL* 4.9 2.0 - - + -
48A ILE* 4.2 24.7 - - + -
51A LEU* 5.4 0.9 - - + -
52A PHE* 4.9 12.3 - - + -
90A LEU* 4.0 17.3 - - + -
91A THR 3.0 6.9 + - - -
92A ILE* 3.2 13.8 - - + +
93A VAL* 2.7 32.3 + - - -
141A CYS* 3.6 15.0 - - + +
143A LEU* 3.8 33.9 - - + -
270A LEU* 4.5 13.7 - - + -
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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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34A LEU* 1.3 76.6 - - - +
36A VAL* 1.3 64.0 + - - +
37A VAL* 3.8 17.5 - - + -
74A VAL* 5.8 1.8 - - + -
93A VAL* 3.4 35.0 - - + +
95A THR* 4.4 4.7 - - - +
111A VAL* 3.6 27.6 - - + +
114A TYR* 4.0 9.4 - - + -
115A ILE* 3.8 24.9 - - + -
139A VAL* 3.8 23.7 - - + +
141A CYS 2.8 18.1 + - - +
142A CYS* 3.4 13.2 - - + -
143A LEU* 2.7 31.5 + - - +
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Residues in contact with VAL 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 LEU* 4.9 3.6 - - + -
35A MET* 1.3 77.7 - - - +
37A VAL* 1.3 63.4 + - - +
38A GLY 4.4 0.3 + - - -
44A LYS* 4.9 15.8 - - + +
48A ILE* 3.9 28.5 - - + -
92A ILE* 4.2 10.8 - - + -
93A VAL 2.9 11.7 + - - +
94A ASP* 3.3 26.5 - - - +
95A THR* 3.3 23.4 + - - +
143A LEU* 3.5 13.0 - - + -
145A PHE* 3.7 25.6 - - + -
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Residues in contact with VAL 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* 3.8 19.7 - - - -
36A VAL* 1.3 75.6 - - - +
38A GLY* 1.3 60.5 + - - +
44A LYS* 4.2 3.4 - - - -
95A THR* 3.4 23.6 - - + +
98A PHE* 3.6 39.5 - - + -
111A VAL* 4.5 2.7 - - + -
142A CYS* 3.9 6.3 - - - -
143A LEU 2.9 11.2 + - - +
144A TYR* 3.3 10.8 - - + -
145A PHE* 3.0 25.5 + - - -
160A PHE* 3.7 30.3 - - + -
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Residues in contact with GLY 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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37A VAL* 1.3 80.9 - - - +
39A GLU* 1.3 68.7 + - - -
40A SER 3.6 0.7 + - - -
44A LYS* 3.1 22.9 + - - +
95A THR* 4.6 2.9 - - - +
98A PHE* 3.4 27.9 + - - +
144A TYR* 4.9 1.6 - - - -
145A PHE* 4.2 14.4 - - - -
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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