Contacts of the strand formed by residues 718 - 728 (chain B) in PDB entry 3RMD
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 THR 718 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714B ASP* 2.7 9.9 - - - +
715B MET* 2.9 32.4 + - - -
716B GLU 3.1 4.5 + - - -
717B GLY* 1.3 71.7 - - - +
719B ARG* 1.3 65.3 + - - +
720B TYR* 3.6 24.8 + - + -
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Residues in contact with ARG 719 (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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645B ASN* 2.8 53.8 + - - +
648B VAL* 3.2 32.7 - - - +
649B ASP* 3.7 22.4 + - - +
652B ASP* 3.6 22.8 + - - +
713B TRP* 3.5 19.1 - - - -
714B ASP* 2.8 20.8 + - - +
717B GLY 3.3 4.1 + - - +
718B THR* 1.3 74.8 - - - +
720B TYR* 1.3 72.7 + - - +
721B ALA 3.8 0.3 + - - -
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Residues in contact with TYR 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B ASN* 5.2 1.7 - - - +
712B VAL* 3.5 37.7 - - + -
713B TRP* 2.9 23.6 + - + +
715B MET* 3.1 30.9 - - + +
718B THR* 4.0 24.0 - - + -
719B ARG* 1.3 85.0 - - - +
721B ALA* 1.3 64.3 + - - +
722B GLU 3.1 19.6 - - - +
723B PRO* 4.7 0.7 - - + -
724B LYS* 3.3 51.5 - - + +
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Residues in contact with ALA 721 (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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713B TRP* 5.4 2.9 - - - -
719B ARG 3.8 1.2 + - - -
720B TYR* 1.3 75.0 - - - +
722B GLU* 1.3 84.7 + - + +
723B PRO* 4.4 2.3 - - - +
76C GLU 5.3 0.5 - - - +
77C ASP 4.7 2.4 - - - +
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Residues in contact with GLU 722 (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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720B TYR* 3.1 18.0 - - - +
721B ALA* 1.3 106.9 - - + +
723B PRO* 1.3 76.6 - - + +
724B LYS* 3.5 6.1 + - - +
76C GLU 3.4 11.6 - - - +
78C ILE 4.7 1.3 - - - +
79C GLY* 3.4 30.3 - - - +
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Residues in contact with PRO 723 (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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711B ASN* 3.6 23.6 - - - +
712B VAL 3.3 13.2 - - - +
713B TRP* 3.7 30.2 - - + -
720B TYR* 4.7 1.6 - - + -
721B ALA 4.5 0.2 - - - +
722B GLU* 1.3 85.1 - - + +
724B LYS* 1.3 61.2 + - - +
725B LEU* 4.2 1.2 + - - +
754B GLN* 3.6 20.8 - - + +
77C ASP 2.9 29.2 - - - +
78C ILE* 4.0 12.7 - - - +
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Residues in contact with LYS 724 (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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712B VAL* 2.9 38.9 + - + +
720B TYR* 3.3 53.3 - - + +
722B GLU 4.0 5.2 - - - +
723B PRO* 1.3 75.5 - - - +
725B LEU* 1.3 68.6 + - - +
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Residues in contact with LEU 725 (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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710B LEU 3.4 2.2 - - - +
711B ASN* 3.5 22.2 - - - +
723B PRO 4.2 1.5 + - - +
724B LYS* 1.3 75.2 - - - +
726B LYS* 1.3 60.2 + - - +
727B ILE* 3.7 21.3 + - + +
746B LYS* 3.7 35.2 - - + +
749B ILE* 4.3 0.9 - - + -
750B ARG* 3.6 41.5 - - + +
753B LEU* 4.2 19.7 - - + -
754B GLN* 3.8 10.3 - - - +
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Residues in contact with LYS 726 (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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626B TYR* 3.6 13.1 + - - -
686B GLU* 6.4 0.7 - - - -
687B ALA* 5.1 3.6 - - + -
708B TYR* 3.1 29.2 + - + +
709B ALA* 3.1 3.8 - - - -
710B LEU* 2.8 46.9 + - + +
712B VAL* 3.6 20.4 - - + -
715B MET* 4.3 26.7 - - + -
724B LYS 3.5 0.6 + - - -
725B LEU* 1.3 71.1 - - - +
727B ILE* 1.3 60.0 + - - +
728B MET* 2.9 38.3 + - + +
115H A 4.2 1.4 + - - -
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Residues in contact with ILE 727 (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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708B TYR 3.5 2.9 - - - +
709B ALA* 3.9 10.5 - - + -
725B LEU* 3.7 25.7 + - + +
726B LYS* 1.3 76.8 - - - +
728B MET* 1.3 72.0 + - - +
730B LEU* 3.5 27.8 - - + -
732B THR* 3.2 28.3 - - + -
733B GLN* 3.0 32.2 - - + +
746B LYS* 4.3 12.6 - - + -
749B ILE* 3.4 34.8 - - + -
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Residues in contact with MET 728 (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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706B LYS 3.8 2.0 - - - -
707B ARG* 3.1 3.6 - - - -
708B TYR* 2.8 60.0 + - + +
726B LYS* 2.9 49.1 + - + +
727B ILE* 1.3 81.9 - - - +
729B GLY* 1.3 59.5 + - - +
730B LEU 2.9 7.9 + - - -
733B GLN* 5.2 1.1 - - - +
114H A 3.4 43.7 - - - +
115H A 3.4 11.0 - - - +
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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