Contacts of the strand formed by residues 262 - 267 (chain 1) in PDB entry 6Q8O
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 GLY 262 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011 PHE* 3.7 16.4 - - - -
2521 TYR 3.9 0.2 - - - +
2531 GLN* 2.9 5.0 - - - -
2541 ILE* 2.9 36.9 + - - +
2611 PRO* 1.3 76.9 - - - +
2631 VAL* 1.3 63.3 + - - -
2641 TYR* 3.9 7.6 - - - -
1292 HIS* 4.1 4.0 - - - -
1752 HIS 3.0 10.1 - - - -
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Residues in contact with VAL 263 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181 TYR* 3.4 51.1 - - + +
1011 PHE* 3.8 30.5 - - + +
1021 LYS* 4.0 14.4 - - + -
1051 TYR* 4.0 10.8 - - + -
2511 LEU* 4.5 6.3 - - + -
2521 TYR 3.4 9.0 - - - +
2531 GLN* 4.3 1.3 - - + -
2621 GLY* 1.3 74.1 - - - -
2641 TYR* 1.3 81.7 + - - +
1752 HIS* 3.2 28.3 + - + +
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Residues in contact with TYR 264 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 ARG* 5.2 5.2 - - - +
181 TYR* 6.0 0.9 - - - -
2511 LEU* 4.5 1.8 - - - -
2521 TYR* 2.9 37.9 + - + +
2531 GLN* 5.5 0.2 - - - -
2541 ILE* 4.8 9.0 - - + -
2601 ARG* 3.0 32.7 + - - +
2621 GLY 3.9 19.3 - - - -
2631 VAL* 1.3 93.8 - - - +
2651 GLU* 1.3 60.0 + - - +
2661 LEU* 3.3 30.9 + - + +
2751 LEU* 5.4 6.1 - - + -
2791 TRP* 3.8 42.2 + + + -
2801 ALA 5.1 0.2 - - - -
1752 HIS* 5.3 3.1 - + - -
1762 VAL* 3.1 28.5 - - + +
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Residues in contact with GLU 265 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131 PHE* 3.2 25.0 - - + -
141 GLU 4.2 2.9 - - - +
151 ARG* 3.4 20.5 + - - +
161 THR* 2.9 19.9 + - - -
171 LEU* 2.6 35.1 + - + +
181 TYR* 2.4 46.8 + - + +
191 ALA 3.7 1.9 + - - -
2491 MET* 4.5 10.9 - - + +
2501 LYS 3.7 4.9 - - - +
2511 LEU* 3.6 21.3 - - + +
2641 TYR* 1.3 69.3 - - - +
2661 LEU* 1.3 65.4 + - - +
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Residues in contact with LEU 266 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 GLY 5.9 0.4 - - - +
131 PHE* 4.1 0.4 - - - -
151 ARG* 3.5 14.8 - - - +
2491 MET* 4.3 4.5 - - - -
2501 LYS* 2.8 32.9 + - - +
2521 TYR* 3.7 18.8 - - + -
2641 TYR* 3.3 26.6 + - + +
2651 GLU* 1.3 83.2 - - - +
2671 PRO* 1.3 78.5 - - + +
2701 THR* 5.1 9.4 - - + +
2751 LEU* 5.0 8.3 - - + -
2791 TRP* 3.4 57.7 - - + +
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Residues in contact with PRO 267 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61 LEU* 4.2 20.4 - - + +
71 SER 4.8 0.2 - - - -
81 GLY* 3.9 33.4 - - - +
131 PHE* 3.7 28.9 - - + -
2411 MET* 4.2 22.4 - - + -
2421 GLY 4.6 0.2 - - - +
2491 MET* 4.1 10.1 - - - -
2521 TYR* 3.6 9.5 - - - -
2661 LEU* 1.3 92.9 - - + +
2681 MET* 1.3 62.6 + - - +
2691 GLY 3.7 1.2 + - - -
2701 THR* 3.8 13.6 - - + +
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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