Contacts of the strand formed by residues 707 - 715 (chain B) in PDB entry 2P5G
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 ARG 707 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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702B TRP* 3.6 0.7 - - - -
703B THR* 2.9 60.6 + - - +
704B GLY* 3.0 15.9 + - - +
705B LYS 3.0 14.8 + - - +
706B LYS* 1.3 78.7 - - + +
708B TYR* 1.3 61.6 + - - +
728B MSE 3.3 5.6 - - - -
729B GLY* 3.2 23.5 + - - +
730B LEU* 3.8 26.4 - - + +
731B GLU* 4.1 10.7 - - - +
882B GLY* 6.0 3.2 - - - -
883B PHE* 4.8 7.7 - - - -
12G G 4.6 15.0 + - - -
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Residues in contact with TYR 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B TYR* 4.0 20.4 - + - -
621B ASP* 5.8 1.1 - - - -
626B TYR* 2.7 27.9 + + - -
701B PHE* 3.3 12.1 - - - +
702B TRP* 3.3 42.2 - + + -
706B LYS* 4.3 5.4 - - - -
707B ARG* 1.3 81.1 - - - +
709B ALA* 1.3 63.4 + - - +
710B LEU* 4.4 11.9 - - + -
726B LYS* 3.0 29.3 + - + -
727B ILE* 3.5 2.4 - - - -
728B MSE 2.8 72.0 + - + +
730B LEU* 4.1 8.8 - - - +
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Residues in contact with ALA 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700B GLY* 3.1 4.5 - - - -
701B PHE* 2.9 63.6 + - + +
708B TYR* 1.3 75.1 - - - +
710B LEU* 1.3 65.1 + - - +
726B LYS 3.4 6.3 - - - -
727B ILE* 4.2 6.7 - - + -
730B LEU* 4.4 2.5 - - + -
749B ILE* 3.8 20.0 - - + -
753B LEU* 3.9 5.2 - - + -
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Residues in contact with LEU 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B VAL* 4.0 22.0 - - + -
409B SER* 5.6 0.4 - - - +
626B TYR* 3.8 30.1 - - + -
687B ALA* 5.1 6.3 - - + -
689B ALA* 3.8 18.2 - - + -
699B GLY 3.7 4.0 - - - -
700B GLY* 4.1 6.3 - - - -
702B TRP* 3.6 27.6 - - + -
708B TYR* 4.4 10.8 - - + -
709B ALA* 1.3 82.5 - - - +
711B ASN* 1.3 58.7 + - - +
712B VAL* 3.5 14.5 + - + -
725B LEU* 3.3 6.8 - - - -
726B LYS* 2.9 40.2 + - + +
727B ILE* 5.4 0.2 - - - +
753B LEU* 3.8 5.6 - - - +
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Residues in contact with ASN 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689B ALA* 3.2 4.4 - - - +
690B GLY 2.9 47.8 + - - +
692B PRO* 4.2 3.4 - - - +
699B GLY* 2.9 17.5 + - - +
710B LEU* 1.3 70.2 - - - +
712B VAL* 1.3 62.1 + - - +
713B TRP* 3.4 28.3 - - - -
723B PRO* 3.9 7.5 - - - +
724B LYS 4.0 2.2 - - - +
725B LEU* 3.6 7.6 - - - +
753B LEU* 4.1 10.5 - - + -
754B GLN* 2.8 44.7 + - - +
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Residues in contact with VAL 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687B ALA* 3.7 33.0 - - + -
688B ILE 3.6 7.2 - - - +
689B ALA* 4.0 2.2 - - + -
710B LEU* 3.9 15.7 - - + -
711B ASN* 1.3 71.0 - - - +
713B TRP* 1.3 63.9 + - - +
714B ASP 3.7 6.7 - - - +
715B MSE 4.1 6.7 - - + -
720B TYR* 3.6 25.8 - - + -
723B PRO* 3.4 6.6 - - - +
724B LYS* 2.9 38.6 + - + +
726B LYS* 3.8 32.3 - - + -
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Residues in contact with TRP 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644B THR* 3.5 28.3 - - + -
645B ASN* 5.8 4.7 - - - -
647B TRP* 3.5 24.2 - + - -
648B VAL* 3.8 22.7 - - + -
688B ILE 2.7 15.2 + - - +
690B GLY 3.0 24.7 + - - -
692B PRO* 3.7 25.4 - - + -
711B ASN* 3.4 34.9 + - - -
712B VAL* 1.3 70.6 - - - +
714B ASP* 1.3 58.1 + - - +
719B ARG* 3.7 7.2 - - - -
720B TYR* 3.0 39.2 + - + +
722B GLU 5.3 0.4 - - - -
723B PRO* 3.6 38.8 - - + -
77C ASP* 3.8 22.2 - - - -
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Residues in contact with ASP 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648B VAL* 4.2 9.4 - - + -
652B ASP* 5.7 0.7 - - - -
685B ARG* 2.3 40.8 + - - +
686B GLU 3.2 1.7 - - - +
687B ALA* 3.2 3.1 - - - -
688B ILE* 3.0 30.5 + - + -
712B VAL* 3.7 3.8 - - - +
713B TRP* 1.3 81.5 - - - +
715B MSE 1.3 59.9 - - - +
717B GLY* 3.1 23.9 + - - +
718B THR 3.5 7.4 - - - -
719B ARG* 2.9 47.2 + - - +
720B TYR* 3.7 2.3 - - - -
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Residues in contact with MSE 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B GLU* 3.0 44.9 - - - +
687B ALA* 3.8 19.3 - - + -
712B VAL* 4.1 10.1 - - + -
714B ASP* 1.3 71.4 - - - +
716B GLU* 1.3 70.2 + - + +
717B GLY 3.0 4.0 - - - -
718B THR* 2.8 40.3 + - - +
720B TYR* 3.1 35.2 - - + +
726B LYS* 4.2 24.0 - - + -
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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