Contacts of the strand formed by residues 748 - 757 (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 THR 748 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665B LEU* 3.6 28.3 - - + -
666B LEU 3.3 6.3 - - - +
667B GLN* 3.4 23.1 + - - +
674B PHE* 3.8 3.9 - - - -
726B ASN* 4.2 6.3 + - - +
742B ILE 4.9 0.9 - - - +
745B GLY* 3.3 28.6 + - - +
746B GLY 3.4 0.2 - - - -
747B ASN* 1.3 82.4 - - - +
749B LEU* 1.3 64.6 + - - +
750B MET 4.9 0.4 - - - +
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Residues in contact with LEU 749 (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 3.6 1.9 - - - +
665B LEU* 3.6 3.4 - - - -
666B LEU* 2.7 46.4 + - + +
674B PHE* 3.6 21.1 - - + -
676B PHE* 3.8 35.4 - - + -
725B VAL* 3.8 29.2 - - + -
726B ASN* 3.7 6.7 - - - +
742B ILE* 3.8 24.9 - - + +
748B THR* 1.3 75.4 - - - +
750B MET* 1.3 62.9 + - - +
751B VAL* 3.8 26.2 - - + -
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Residues in contact with MET 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B THR* 3.8 29.4 - - + -
664B VAL 3.5 4.0 - - - +
665B LEU* 3.6 25.1 - - + +
724B GLU* 3.7 9.7 - - - +
725B VAL* 3.5 3.6 - - - -
726B ASN* 2.8 53.0 + - - +
727B GLY* 5.4 4.3 - - - +
748B THR* 5.7 0.2 - - + -
749B LEU* 1.3 73.8 - - - +
751B VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 751 (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 3.9 0.5 - - - +
663B THR* 3.3 7.1 - - - +
664B VAL* 3.0 54.4 + - + +
666B LEU* 4.9 4.0 - - + -
676B PHE* 5.9 1.1 - - + -
716B LEU* 4.4 12.6 - - + -
722B LEU* 4.3 16.4 - - + -
724B GLU 3.2 10.5 - - - +
725B VAL* 4.2 9.9 - - + -
749B LEU* 3.8 35.0 - - + -
750B MET* 1.3 73.5 - - - +
752B LYS* 1.3 59.4 + - - +
753B VAL* 4.1 17.7 - - + -
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Residues in contact with LYS 752 (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* 3.7 28.8 + - + +
662B LYS 3.5 10.5 - - - +
663B THR* 3.1 20.6 - - - +
722B LEU* 3.8 1.4 - - - -
723B ILE* 2.9 41.2 + - + +
724B GLU* 3.0 48.6 + - + +
751B VAL* 1.3 74.0 - - - +
753B VAL* 1.3 64.3 + - - +
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Residues in contact with VAL 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B GLU* 3.3 7.1 - - - +
662B LYS* 3.1 43.7 + - + +
664B VAL* 5.7 0.7 - - + -
702B LEU* 5.3 0.9 - - + -
716B LEU* 4.0 30.5 - - + -
720B ASP* 4.1 21.5 - - + +
721B PHE 2.9 20.4 - - - +
722B LEU* 4.3 12.3 - - + -
723B ILE* 4.5 1.1 - - - +
751B VAL* 4.0 18.4 - - + -
752B LYS* 1.3 78.6 - - - +
754B VAL* 1.3 61.4 + - - +
755B MET* 4.0 10.7 + - + -
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Residues in contact with VAL 754 (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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694A PRO* 6.1 0.4 - - + -
659B ILE* 3.5 31.0 - - + -
660B LYS 3.6 3.8 - - - +
661B GLU* 3.9 19.7 - - + +
697B PRO* 4.1 20.9 - - + -
720B ASP* 3.5 5.4 - - - -
721B PHE* 2.9 32.5 + - + -
723B ILE* 3.2 33.2 - - + -
753B VAL* 1.3 75.6 - - - +
755B MET* 1.3 63.0 + - - +
756B VAL* 3.8 17.5 + - + -
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Residues in contact with MET 755 (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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658B ILE 3.3 5.0 - - - +
659B ILE* 3.4 2.1 - - - -
660B LYS* 2.6 64.5 + - + +
662B LYS* 3.7 39.9 - - - +
715B GLY 5.3 1.3 - - - +
720B ASP* 3.4 27.1 - - - +
753B VAL* 4.4 7.0 - - + +
754B VAL* 1.3 72.3 - - - +
756B VAL* 1.3 60.9 + - - +
757B THR* 3.9 19.2 - - + +
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Residues in contact with VAL 756 (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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657B TYR* 3.7 37.2 - - + -
658B ILE 3.2 3.1 - - - -
659B ILE* 3.3 20.2 - - + -
694B PRO 4.1 9.6 - - - +
695B ALA* 4.7 9.2 - - + +
697B PRO* 4.7 0.4 - - + -
719B GLY 5.1 6.0 + - - +
720B ASP* 4.9 1.4 + - - -
721B PHE* 4.3 24.5 - - + -
754B VAL* 3.8 14.5 + - + -
755B MET* 1.3 76.0 - - - +
757B THR* 1.3 59.2 + - - +
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Residues in contact with THR 757 (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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657B TYR* 3.1 9.3 - - - +
658B ILE* 3.0 47.5 + - - +
717B ARG* 6.0 3.4 - - - +
755B MET* 4.6 21.8 - - + +
756B VAL* 1.3 79.4 - - - +
758B ARG* 1.3 67.9 + - - +
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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