Contacts of the helix formed by residues 648 - 662 (chain D) in PDB entry 2GL7
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 ASN 648 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D GLU* 3.9 24.4 - - + +
609D ASN* 4.9 5.5 - - - +
612D ARG* 5.6 2.7 - - - +
643D LEU 4.9 0.5 - - - +
646D SER* 3.1 11.2 + - - +
647D ARG* 1.3 76.0 - - - +
649D GLU* 1.3 61.8 + - - +
650D GLY* 3.4 15.4 - - - +
651D VAL* 3.5 27.9 + - + +
652D ALA* 3.3 19.9 + - - +
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Residues in contact with GLU 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646D SER 4.8 1.6 - - - -
647D ARG 3.2 6.9 + - - +
648D ASN* 1.3 71.4 - - - +
650D GLY* 1.3 58.4 + - - +
651D VAL 3.4 0.2 - - - -
652D ALA* 3.8 9.0 - - - +
653D THR* 2.6 34.9 + - - +
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Residues in contact with GLY 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D ARG* 5.1 4.9 - - - -
648D ASN* 3.3 10.9 - - - +
649D GLU* 1.3 75.9 - - - +
651D VAL* 1.3 63.1 + - - +
653D THR* 3.5 5.9 + - - -
654D TYR* 3.4 35.2 + - - -
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Residues in contact with VAL 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608D GLU* 3.8 10.1 - - + +
611D GLN* 4.2 26.0 - - + +
612D ARG* 3.6 35.0 - - + +
615D ALA* 4.8 3.2 - - + +
643D LEU* 3.7 29.2 - - + +
646D SER* 6.1 2.2 - - - -
648D ASN* 3.5 30.7 + - + +
649D GLU 3.4 0.2 - - - -
650D GLY* 1.3 76.2 - - - +
652D ALA* 1.3 57.6 + - - +
654D TYR* 3.6 3.4 + - - +
655D ALA* 3.1 26.7 + - + +
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Residues in contact with ALA 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643D LEU 3.6 14.4 - - - +
644D LEU* 3.4 26.6 - - - +
646D SER 4.6 5.4 - - - +
648D ASN 3.3 13.4 + - - +
649D GLU* 3.9 9.0 - - - +
650D GLY 3.3 0.4 - - - -
651D VAL* 1.3 76.8 - - - +
653D THR* 1.3 64.1 + - - +
655D ALA* 3.9 1.0 - - - +
656D ALA* 3.4 24.8 + - - +
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Residues in contact with THR 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649D GLU* 2.6 24.3 + - - +
650D GLY* 3.9 6.9 - - - -
651D VAL 3.3 0.2 - - - -
652D ALA* 1.3 77.8 - - - +
654D TYR* 1.3 67.8 + - + +
656D ALA* 4.4 1.7 - - - +
657D ALA* 3.2 22.7 + - - +
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Residues in contact with TYR 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D HIS* 3.6 33.5 + + - -
612D ARG* 3.8 20.4 - - + -
615D ALA* 4.0 24.5 - - + +
616D GLY* 3.8 7.2 - - - -
619D CYS* 3.9 21.7 - - + -
620D GLU* 5.8 2.5 - - + -
650D GLY* 3.4 24.2 + - - +
651D VAL 4.2 1.1 - - - +
653D THR* 1.3 83.8 - - + +
655D ALA* 1.3 58.8 + - - +
657D ALA* 3.5 5.1 + - + +
658D VAL* 3.1 26.2 + - - +
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Residues in contact with ALA 655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D ALA* 4.5 10.5 - - + +
640D LEU* 3.5 48.3 - - + +
643D LEU* 3.9 15.0 - - + -
644D LEU* 4.2 5.4 - - - +
651D VAL 3.1 18.8 + - - +
652D ALA 4.2 3.6 - - - +
653D THR 3.3 0.4 - - - -
654D TYR* 1.3 73.8 - - - +
656D ALA* 1.3 64.5 + - - +
657D ALA 3.2 1.3 - - - -
658D VAL* 3.3 11.1 + - - +
659D LEU* 3.7 4.6 + - - +
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Residues in contact with ALA 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644D LEU* 4.6 13.4 - - + +
652D ALA 3.4 16.1 + - - +
653D THR* 4.7 1.8 - - - +
655D ALA* 1.3 77.2 - - - +
657D ALA* 1.3 62.0 + - - +
659D LEU* 3.5 14.9 + - + +
660D PHE* 3.3 20.1 + - - +
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Residues in contact with ALA 657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D CYS* 3.6 21.1 - - - -
653D THR 3.2 20.7 + - - +
654D TYR* 3.6 7.9 - - + +
655D ALA 3.2 0.8 - - - -
656D ALA* 1.3 78.4 - - - +
658D VAL* 1.3 59.6 + - - +
659D LEU 3.2 0.7 - - - -
660D PHE* 3.4 10.1 + - - +
661D ARG* 3.4 22.3 + - - +
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Residues in contact with VAL 658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D ALA* 5.2 4.0 - - + +
618D LEU* 5.0 9.9 - - + +
619D CYS* 4.9 18.6 - - - +
622D ALA* 5.0 4.7 - - + +
631D ILE* 5.0 8.1 - - + +
640D LEU* 3.7 25.2 - - + +
654D TYR 3.1 13.2 + - - +
655D ALA* 3.7 3.4 - - - +
656D ALA 3.3 0.6 - - - -
657D ALA* 1.3 76.0 - - - +
659D LEU* 1.3 60.0 + - - +
661D ARG* 4.2 4.5 - - - +
662D MET* 3.2 27.9 + - - +
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Residues in contact with LEU 659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637D THR* 4.1 23.8 - - + +
640D LEU* 3.6 37.2 - - + +
641D THR* 4.9 11.4 - - - -
644D LEU* 5.7 3.1 - - + -
655D ALA 3.7 9.8 + - - +
656D ALA* 3.5 14.3 + - + +
657D ALA 3.2 0.6 - - - -
658D VAL* 1.3 77.2 - - - +
660D PHE* 1.3 64.2 + - - +
661D ARG 3.3 1.8 - - - -
662D MET* 3.1 25.8 - - + +
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Residues in contact with PHE 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656D ALA 3.3 11.9 + - - +
657D ALA* 3.4 13.6 + - - +
659D LEU* 1.3 80.0 - - - +
661D ARG* 1.3 59.3 - - - +
662D MET 4.9 1.0 - - - +
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Residues in contact with ARG 661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D CYS 5.4 0.7 - - - +
622D ALA* 3.5 40.4 - - + +
623D GLN* 5.6 0.4 - - - -
628D ALA* 3.8 12.9 - - - +
657D ALA 3.4 12.5 + - - +
658D VAL 4.5 0.9 - - - +
660D PHE* 1.3 79.3 - - - +
662D MET* 1.3 59.6 + - - +
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Residues in contact with MET 662 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622D ALA* 5.6 1.3 - - + -
628D ALA* 3.5 32.5 - - + +
631D ILE* 4.1 12.1 - - + -
632D GLU* 5.4 5.4 - - + -
658D VAL 3.2 20.3 + - - +
659D LEU* 3.1 27.3 + - + +
660D PHE 4.9 1.0 - - - +
661D ARG* 1.3 80.8 - - + +
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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