Contacts of the strand formed by residues 655 - 667 (chain B) in PDB entry 3QJM
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 SER 655 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659A ILE 3.9 0.3 - - - +
661A GLU* 2.8 57.1 + - - +
654B GLY* 1.3 73.0 - - - -
656B ASP* 1.3 66.2 + - - +
657B TYR* 3.8 22.4 - - - -
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Residues in contact with ASP 656 (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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658A ILE* 5.0 4.9 - - - +
659A ILE 3.4 8.0 - - - +
660A LYS* 3.4 37.4 - - - +
654B GLY 4.2 3.1 + - - +
655B SER* 1.3 85.2 + - - +
657B TYR* 1.3 66.3 + - - +
758B ARG* 3.1 42.7 + - - +
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Residues in contact with TYR 657 (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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658A ILE* 3.7 2.3 - - - +
659A ILE* 2.7 76.7 + - + +
661A GLU* 2.8 37.4 + - + +
754A VAL* 4.3 1.6 - - - +
655B SER* 3.8 19.5 - - - -
656B ASP* 1.3 80.1 - - - +
658B ILE* 1.3 61.9 + - - +
659B ILE* 4.0 7.6 - - + -
694B PRO* 3.8 18.4 - - + +
695B ALA* 3.7 22.8 + - + +
756B VAL* 3.7 24.0 - - + -
757B THR 3.1 16.6 - - - +
758B ARG* 3.8 9.0 - - - +
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Residues in contact with ILE 658 (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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656A ASP* 4.2 26.0 - - + +
657A TYR 3.4 9.2 - - - +
658A ILE* 4.1 15.9 - - + -
758A ARG* 6.0 1.3 - - - +
657B TYR* 1.3 79.4 - - - +
659B ILE* 1.3 72.2 + - - +
660B LYS* 5.1 4.0 - - + +
755B MET 3.3 1.6 - - - +
756B VAL* 3.2 6.4 - - - -
757B THR* 3.0 44.8 + - - +
758B ARG* 3.7 37.0 - - + +
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Residues in contact with ILE 659 (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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656A ASP* 3.5 4.0 - - - -
657A TYR* 2.8 47.2 + - + +
659A ILE* 3.9 22.4 - - + -
694A PRO* 4.3 26.2 - - + -
657B TYR* 4.0 4.9 - - + -
658B ILE* 1.3 74.7 - - - +
660B LYS* 1.3 68.1 + - - +
661B GLU* 5.1 3.4 - - + -
694B PRO* 3.6 20.2 - - + +
754B VAL* 3.5 20.0 - - + -
755B MET 3.4 0.9 - - - -
756B VAL* 3.3 39.0 - - + -
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Residues in contact with LYS 660 (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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656A ASP* 2.7 35.0 - - - +
657A TYR* 5.7 1.3 - - - -
658B ILE* 5.1 4.3 - - + +
659B ILE* 1.3 78.1 - - - +
661B GLU* 1.3 73.5 + - - +
754B VAL* 3.5 1.2 - - - -
755B MET* 2.6 66.3 + - + +
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Residues in contact with GLU 661 (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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657A TYR* 6.5 1.1 - - + -
694A PRO* 4.0 22.6 - - + +
659B ILE* 5.1 2.2 - - + -
660B LYS* 1.3 94.0 + - - +
662B LYS* 1.3 66.6 + - - +
723B ILE* 5.3 2.3 - - - +
752B LYS* 3.7 29.5 + - + +
753B VAL 3.3 7.2 - - - +
754B VAL* 3.9 29.6 - - + +
755B MET* 5.5 1.1 - - - -
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Residues in contact with LYS 662 (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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661B GLU* 1.3 78.3 - - - +
663B THR* 1.3 64.7 + - - +
664B VAL* 4.3 20.5 + - + +
714B ALA 4.4 2.4 + - - -
715B GLY* 2.9 36.8 + - - -
716B LEU* 4.7 8.1 - - - -
720B ASP* 5.6 0.2 - - - -
751B VAL 3.9 0.5 - - - +
752B LYS* 3.5 4.9 - - - +
753B VAL* 3.1 34.4 + - + +
755B MET* 3.7 28.8 - - - +
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Residues in contact with THR 663 (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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662B LYS* 1.3 75.3 - - - +
664B VAL* 1.3 72.8 + - - +
750B MET* 3.8 36.5 - - + +
751B VAL 3.3 10.1 - - - +
752B LYS* 3.1 26.7 - - + +
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Residues in contact with VAL 664 (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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662B LYS* 4.3 22.9 - - + +
663B THR* 1.3 85.5 - - - +
665B LEU* 1.3 59.5 + - - +
666B LEU* 3.9 12.1 + - + -
714B ALA* 4.0 21.3 - - + +
716B LEU* 3.6 24.2 - - + -
749B LEU 3.6 2.3 - - - +
750B MET* 3.5 2.4 - - - +
751B VAL* 3.0 49.0 + - + +
753B VAL* 5.6 0.7 - - + -
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Residues in contact with LEU 665 (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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664B VAL* 1.3 73.8 - - - +
666B LEU* 1.3 61.6 + - - +
667B GLN* 3.9 21.1 + - - +
714B ALA* 5.4 2.3 - - - +
748B THR* 3.6 26.9 - - + -
749B LEU 3.6 1.8 - - - +
750B MET* 3.6 32.1 - - + -
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Residues in contact with LEU 666 (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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664B VAL* 4.3 15.9 - - + +
665B LEU* 1.3 74.4 - - - +
667B GLN* 1.3 63.9 + - - +
668B LYS 4.1 0.2 - - - -
674B PHE* 3.8 28.8 - - + -
676B PHE* 4.2 8.7 - - + -
710B VAL* 4.1 7.6 - - + +
711B ALA* 4.2 13.0 - - + -
714B ALA* 3.4 33.0 - - + -
716B LEU* 4.1 20.9 - - + -
747B ASN 3.6 0.7 - - - +
748B THR* 3.3 8.3 - - - +
749B LEU* 2.7 54.0 + - + +
751B VAL* 4.9 2.9 - - + -
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Residues in contact with GLN 667 (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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665B LEU* 3.9 22.4 + - - +
666B LEU* 1.3 76.8 - - - +
668B LYS* 1.3 62.9 + - - +
672B GLU* 4.8 0.3 - - - +
710B VAL* 3.7 18.2 - - - +
713B ARG* 5.1 2.8 + - - -
747B ASN 3.7 2.9 - - - +
748B THR* 3.4 22.9 + - - +
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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