Contacts of the strand formed by residues 640 - 649 (chain B) in PDB entry 1LQF
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 LEU 640 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596B TRP* 3.5 39.9 - - + +
597B GLU* 3.5 12.8 - - + +
600B TRP* 4.1 26.7 - - + -
634B ILE* 3.6 2.3 - - - -
635B PHE* 3.0 38.9 + - + -
638B THR* 3.7 20.6 - - - +
639B ASN* 1.3 82.5 - - - +
641B LYS* 1.3 60.6 + - - +
660B LEU* 4.1 12.8 - - + -
661B GLU 3.3 14.4 - - - +
662B ASN* 3.9 13.5 - - + -
663B LEU* 3.9 6.2 - - - +
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Residues in contact with LYS 641 (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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632B GLU* 3.6 34.1 + - + +
633B MET 3.4 4.3 - - - +
634B ILE* 3.7 21.3 - - + -
640B LEU* 1.3 75.1 - - - +
642B LEU* 1.3 63.0 + - - +
643B THR* 4.7 9.9 - - - +
659B GLU 3.7 1.1 - - - +
660B LEU* 3.3 6.8 - - - +
661B GLU* 2.8 63.6 + - + +
663B LEU* 3.9 21.4 - - + +
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Residues in contact with LEU 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B TRP* 3.4 49.6 - - + +
624B TYR 3.6 9.9 - - - +
625B TRP* 4.0 0.9 - - + -
626B PRO* 3.6 24.3 - - + +
632B GLU* 3.5 1.0 - - - +
633B MET* 2.7 44.6 + - + +
635B PHE* 4.0 13.7 - - + -
641B LYS* 1.3 74.5 - - - +
643B THR* 1.3 69.7 + - - +
658B LEU* 3.8 25.1 - - + -
659B GLU 3.6 6.1 - - - +
660B LEU* 4.3 20.2 - - + -
671B ILE* 5.8 0.2 - - + -
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Residues in contact with THR 643 (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 PRO* 4.0 2.0 - - - -
629B GLU 4.1 3.4 - - - +
630B GLU* 4.9 7.6 - - - +
631B LYS 4.1 13.9 - - - +
632B GLU* 4.1 12.0 - - + +
641B LYS* 4.7 12.5 - - - -
642B LEU* 1.3 79.8 + - - +
644B LEU* 1.3 74.7 + - - +
645B ILE* 4.0 12.3 - - + +
658B LEU* 3.1 10.5 - - - -
659B GLU* 2.9 39.8 + - - -
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Residues in contact with LEU 644 (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 PRO* 3.7 29.2 - - + +
627B GLN 3.4 26.0 - - - +
629B GLU* 3.3 45.9 - - + +
630B GLU* 4.5 1.2 - - - +
631B LYS 4.1 0.6 + - - -
643B THR* 1.3 81.4 - - - +
645B ILE* 1.3 61.5 + - - +
646B SER 3.3 25.6 - - - +
647B GLU* 4.4 14.6 - - + +
656B ARG* 3.8 29.4 - - + -
657B GLN 3.9 0.7 - - - +
658B LEU* 3.7 14.1 - - + -
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Residues in contact with ILE 645 (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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629B GLU* 3.4 27.3 - - - +
630B GLU* 5.9 1.3 - - - +
643B THR* 4.0 19.1 - - + +
644B LEU* 1.3 82.0 - - - +
646B SER* 1.3 62.1 + - - +
657B GLN* 2.7 51.6 + - + +
658B LEU 4.3 1.1 - - - -
659B GLU* 4.2 22.4 - - + +
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Residues in contact with SER 646 (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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629B GLU* 5.2 2.2 - - - -
644B LEU* 3.3 13.6 - - - +
645B ILE* 1.3 81.1 - - - +
647B GLU* 1.3 66.9 + - - +
648B ASP* 6.3 0.7 - - - -
655B VAL 5.2 0.9 + - - -
656B ARG* 3.4 0.9 - - - -
657B GLN* 3.1 48.8 + - - +
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Residues in contact with GLU 647 (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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627B GLN* 4.3 13.9 - - - +
644B LEU* 4.4 12.1 - - + +
646B SER* 1.3 81.1 + - - +
648B ASP* 1.3 60.1 + - - +
649B ILE* 3.6 20.5 + - + +
654B THR* 3.8 18.8 - - + -
655B VAL 3.2 7.8 + - - -
656B ARG* 2.9 34.3 + - + +
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Residues in contact with ASP 648 (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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646B SER* 6.3 0.9 - - - -
647B GLU* 1.3 71.9 - - - +
649B ILE* 1.3 64.6 + - - +
650B LYS* 3.1 40.6 + - - +
654B THR* 4.2 0.2 - - - -
655B VAL* 2.7 30.1 + - + +
697B LYS* 5.5 0.9 - - - -
736C ASP* 4.3 15.6 - - - +
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Residues in contact with ILE 649 (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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647B GLU* 3.5 23.4 + - + +
648B ASP* 1.3 79.7 - - - +
650B LYS* 1.3 78.2 + - - +
654B THR* 3.1 36.6 - - + +
656B ARG* 5.1 3.1 - - - +
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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