Contacts of the helix formed by residues 683 - 696 (chain A) in PDB entry 1Q2L
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 683 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631A GLU* 6.0 1.1 - - - -
634A LEU* 4.9 3.1 - - - -
681A SER 3.8 10.8 - - - +
682A ILE* 1.3 79.1 - - - +
684A LEU* 1.3 64.7 + - - +
685A LYS* 3.6 14.9 + - - +
686A GLU* 3.1 37.5 + - - +
687A VAL* 3.1 24.6 + - - +
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Residues in contact with LEU 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A LEU* 4.0 15.5 - - + -
629A ALA* 3.5 41.1 - - + +
630A THR 4.5 0.2 - - - -
631A GLU* 3.6 41.5 + - + +
634A LEU* 4.3 22.1 - - + +
683A THR* 1.3 73.8 - - - +
685A LYS* 1.3 56.7 + - - +
687A VAL* 3.2 5.2 + - + -
688A LEU* 2.9 66.9 + - + +
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Residues in contact with LYS 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683A THR* 3.6 13.0 + - - +
684A LEU* 1.3 81.1 - - - +
686A GLU* 1.3 76.8 + - - +
688A LEU* 3.5 9.8 + - - +
689A ALA* 3.0 27.1 + - + +
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Residues in contact with GLU 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A ARG* 3.0 30.2 + - - -
568A MET* 3.7 15.8 - - + +
681A SER 3.7 6.4 - - - +
682A ILE* 3.5 2.9 - - - +
683A THR* 3.1 37.3 + - - +
685A LYS* 1.3 92.3 + - - +
687A VAL* 1.3 59.5 + - - +
689A ALA* 3.1 7.9 + - - +
690A TYR* 2.8 29.6 + - - +
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Residues in contact with VAL 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A MET* 4.3 8.1 - - + +
571A LEU* 4.4 14.4 - - + -
572A ASN* 3.8 34.9 + - + +
575A LEU* 4.4 9.6 - - + -
627A TYR* 4.0 9.9 - - - +
634A LEU* 4.4 9.2 - - + -
682A ILE* 3.5 21.5 - - + -
683A THR 3.1 14.6 + - - +
684A LEU* 3.2 9.4 + - + +
686A GLU* 1.3 76.1 - - - +
688A LEU* 1.3 61.3 + - + +
690A TYR* 3.2 7.8 + - - +
691A ARG* 2.9 27.9 + - - +
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Residues in contact with LEU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A TYR* 4.5 20.2 - - + +
629A ALA* 5.2 4.0 - - + +
684A LEU* 2.9 57.5 + - + +
685A LYS* 3.8 8.1 - - - +
687A VAL* 1.3 77.9 - - + +
689A ALA* 1.3 60.8 + - - +
691A ARG* 3.4 26.1 - - - +
692A ASP* 2.9 30.3 + - - +
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Residues in contact with ALA 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A LYS* 3.0 20.1 + - + +
686A GLU* 3.1 7.4 + - - +
688A LEU* 1.3 73.9 - - - +
690A TYR* 1.3 66.7 + - - +
692A ASP* 3.4 7.5 + - - +
693A ALA* 3.1 21.8 + - - +
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Residues in contact with TYR 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A ALA* 2.7 45.9 + - + +
560A MET* 4.2 0.7 - - - +
565A ASN* 3.5 35.7 - - - -
568A MET* 3.8 33.9 - - + -
569A PHE* 3.4 40.1 - + + +
572A ASN* 4.7 4.7 - - + -
686A GLU 2.8 13.8 + - - +
687A VAL 3.2 8.3 + - - +
689A ALA* 1.3 77.0 - - - +
691A ARG* 1.3 60.0 + - - +
693A ALA* 3.0 10.8 + - + +
694A LEU* 2.8 45.7 + - + +
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Residues in contact with ARG 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A ASN* 3.2 37.7 - - - +
624A TYR 3.5 14.6 - - - +
625A PHE* 3.4 48.6 + - + +
626A SER* 4.1 4.0 - - - +
627A TYR* 2.8 56.0 + - - +
687A VAL 2.9 9.4 + - - +
688A LEU* 3.4 28.0 + - - +
689A ALA 3.2 0.2 - - - -
690A TYR* 1.3 80.9 - - - +
692A ASP* 1.3 75.6 + - - +
694A LEU* 3.1 21.2 - - - +
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Residues in contact with ASP 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A PHE* 5.0 3.6 - - - +
688A LEU* 2.9 20.8 + - - +
689A ALA* 3.9 8.1 - - - +
690A TYR 3.3 0.4 - - - -
691A ARG* 1.3 95.1 + - - +
693A ALA* 1.3 61.8 + - - +
695A LYS* 3.6 27.6 + - - +
696A SER* 3.2 23.8 + - - -
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Residues in contact with ALA 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A ASN* 3.1 7.4 - - - +
558A LYS* 3.6 10.9 + - - +
559A ALA* 5.4 1.3 - - - +
689A ALA 3.1 12.5 + - - +
690A TYR* 3.0 15.5 + - + +
692A ASP* 1.3 75.3 - - - +
694A LEU* 1.3 64.6 + - - +
696A SER* 3.1 26.6 - - - +
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Residues in contact with LEU 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A LEU* 4.9 3.0 - - + +
556A ASN* 2.8 21.0 - - - +
559A ALA* 4.1 22.2 - - + -
569A PHE* 4.0 25.4 - - + -
572A ASN* 4.3 9.0 - - - +
601A GLY* 4.4 3.4 - - - -
602A LEU* 3.9 33.0 - - + +
624A TYR* 4.2 12.3 - - + -
625A PHE* 4.0 17.7 - - + -
690A TYR* 2.8 26.3 + - + +
691A ARG* 3.1 12.7 + - - +
693A ALA* 1.3 78.5 - - - +
695A LYS* 1.3 60.4 + - - +
698A ALA* 3.5 8.7 - - - +
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Residues in contact with LYS 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A LEU* 4.3 11.4 - - + -
625A PHE* 3.6 52.3 - - + -
691A ARG 4.4 0.2 - - - +
692A ASP* 3.6 26.3 + - - +
694A LEU* 1.3 78.0 - - - +
696A SER* 1.3 66.5 + - - +
697A GLY 3.5 0.3 + - - -
698A ALA* 3.5 10.6 + - - +
723A GLN 5.4 1.7 + - - -
724A LEU* 3.2 43.9 + - + +
726A ALA* 3.4 25.6 - - - +
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Residues in contact with SER 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A ASN* 3.7 4.5 - - - +
558A LYS* 3.8 8.5 + - - -
692A ASP 3.2 19.3 + - - -
693A ALA* 3.1 21.3 - - - +
694A LEU 3.3 0.6 - - - -
695A LYS* 1.3 76.5 - - - +
697A GLY* 1.3 60.8 + - - +
698A ALA 3.1 4.5 + - - -
724A LEU 6.0 0.2 - - - -
725A GLY 5.3 5.2 - - - -
730A GLU* 4.5 0.3 - - - +
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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