Contacts of the strand formed by residues 189 - 194 (chain A) in PDB entry 2P4G
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 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A THR 4.3 1.1 - - - -
29A THR* 2.9 36.6 + - - +
31A ASN* 4.8 2.7 - - - +
32A GLU 3.0 30.3 - - - +
34A GLU* 3.3 11.4 + - + +
71A TRP* 3.5 62.0 - - + +
72A ALA 3.7 0.2 - - - -
73A ASP* 2.7 46.9 + - - +
74A ALA 3.1 8.7 + - - +
105A ARG* 4.7 2.5 - - - +
188A LYS* 1.3 74.0 - - + +
190A ILE* 1.3 61.1 + - - +
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Residues in contact with ILE 190 (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 GLU 2.9 10.6 + - - +
35A CYS* 3.3 9.1 - - + -
36A ARG 2.9 27.4 + - - +
71A TRP* 3.6 5.8 - - - -
74A ALA* 3.4 9.6 - - + +
76A VAL* 3.6 30.3 - - + -
179A PHE* 3.7 22.0 - - + +
182A LEU* 4.0 25.6 - - + -
183A HIS* 3.6 29.6 - - + +
187A LEU 4.1 10.1 - - - +
188A LYS 4.3 3.1 - - - +
189A LYS* 1.3 76.8 - - - +
191A SER* 1.3 65.6 + - - +
192A ILE* 4.6 7.4 - - + -
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Residues in contact with SER 191 (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 ARG 3.2 4.3 - - - -
38A ILE* 3.7 11.3 - - - +
65A LEU* 5.3 0.3 - - - +
68A LEU* 3.4 28.1 - - - +
69A ARG 5.4 0.6 + - - -
71A TRP* 3.9 9.3 - - - -
72A ALA* 4.0 18.8 - - - -
74A ALA 2.9 8.3 + - - -
75A ILE* 3.2 9.8 - - - +
76A VAL 2.8 31.9 + - - +
190A ILE* 1.3 73.6 - - - +
192A ILE* 1.3 55.7 + - - +
193A GLU* 3.8 9.8 + - - +
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Residues in contact with ILE 192 (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 CYS* 3.8 27.1 - - - -
36A ARG 2.7 11.8 + - - +
37A ALA* 3.3 5.4 - - + -
38A ILE 2.8 28.9 + - - +
76A VAL* 3.2 18.6 - - + +
175A LEU* 4.5 12.3 - - + -
190A ILE* 4.6 3.1 - - + -
191A SER* 1.3 73.0 + - - +
193A GLU* 1.3 61.0 + - - +
194A GLY 3.6 7.8 + - - +
198A VAL* 3.6 27.1 - - + -
199A TYR* 3.8 16.5 - - + +
202A ALA* 3.5 31.2 - - + -
207A ILE* 4.7 2.9 - - + -
208A VAL* 4.4 4.5 - - + -
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Residues in contact with GLU 193 (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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38A ILE* 3.8 21.5 - - + -
65A LEU* 3.4 20.0 - - + +
69A ARG* 2.7 45.5 + - - +
75A ILE* 3.3 21.2 - - + +
76A VAL 2.9 9.9 + - - +
77A VAL* 4.1 9.1 - - + +
81A THR* 4.5 4.0 - - - +
87A TYR* 2.5 37.9 + - - +
191A SER* 3.8 7.9 + - - +
192A ILE* 1.3 71.2 - - - +
194A GLY* 1.3 58.8 + - - +
195A GLY 4.1 0.5 + - - -
199A TYR* 3.1 13.5 + - - -
278A EDO 3.3 13.7 + - - +
280A EDO 4.2 2.1 + - - -
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Residues in contact with GLY 194 (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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76A VAL 3.9 1.4 + - - -
77A VAL* 3.5 5.9 - - - +
78A GLY 2.9 29.3 + - - -
192A ILE* 3.2 6.8 - - - +
193A GLU* 1.3 81.6 - - - +
195A GLY* 1.3 61.6 - - - -
198A VAL* 3.4 9.6 - - - +
199A TYR* 3.3 25.8 - - - -
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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