Contacts of the helix formed by residues 646 - 661 (chain A) in PDB entry 6DGD
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 GLN 646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644A ASN* 2.8 14.5 + - + +
645A ASN* 1.3 85.5 + - - +
647A GLN* 1.3 62.4 + - - +
649A PRO* 3.4 5.8 - - - +
650A LEU* 2.9 52.0 - - + +
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Residues in contact with GLN 647 (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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642A ASP* 3.0 8.4 + - - +
644A ASN* 3.3 30.4 + - - +
646A GLN* 1.3 77.9 - - + +
648A ALA* 1.3 67.6 + - - +
650A LEU* 3.6 2.1 + - - +
651A PHE* 3.2 23.5 + - + +
716A GLU* 4.9 8.8 + - + +
719A LYS* 2.9 46.9 + - - +
720A VAL* 3.5 11.3 - - + +
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Residues in contact with ALA 648 (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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640A ALA* 3.9 25.8 - - + +
641A GLU* 4.0 6.3 - - - -
642A ASP* 2.5 36.3 + - + +
647A GLN* 1.3 75.2 - - - +
649A PRO* 1.3 65.2 - - + +
651A PHE* 3.4 2.6 + - - +
652A LEU* 3.1 26.2 + - - +
688A TRP* 4.6 6.3 - - + -
720A VAL* 3.7 14.4 - - + -
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Residues in contact with PRO 649 (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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642A ASP* 3.9 1.8 - - - +
645A ASN 3.2 21.5 - - - +
646A GLN* 3.4 14.8 - - - +
647A GLN 3.4 4.5 - - - -
648A ALA* 1.3 94.2 - - + +
650A LEU* 1.3 61.8 + - + +
652A LEU* 3.0 10.3 + - + +
653A GLN* 2.9 23.1 + - - -
674A PRO* 3.5 11.1 - - + +
688A TRP* 3.3 50.0 - - + +
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Residues in contact with LEU 650 (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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646A GLN* 2.9 49.1 - - + +
647A GLN* 3.6 2.2 + - - +
648A ALA 3.4 0.4 - - - -
649A PRO* 1.3 83.9 - - + +
651A PHE* 1.3 66.3 + - - +
653A GLN* 3.2 13.9 + - + +
654A GLN* 3.0 34.5 + - + +
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Residues in contact with PHE 651 (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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638A ILE* 5.8 0.7 - - + -
640A ALA* 4.4 2.5 - - + -
647A GLN 3.2 18.7 + - - +
648A ALA 3.7 3.6 - - - +
650A LEU* 1.3 76.6 - - - +
652A LEU* 1.3 83.5 + - + +
654A GLN* 3.3 12.1 + - - +
655A LEU* 3.2 36.1 + - + +
711A ILE* 4.6 3.1 - - + -
714A LEU* 4.1 17.9 - - + -
716A GLU* 3.7 27.8 - - + +
717A ALA* 3.5 33.9 - - + -
720A VAL* 3.4 27.8 - - + -
722A TRP* 4.2 21.8 - + + -
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Residues in contact with LEU 652 (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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638A ILE* 4.2 20.2 - - + +
640A ALA* 3.7 14.6 - - + +
648A ALA 3.1 11.7 + - - +
649A PRO 3.0 8.1 + - - +
651A PHE* 1.3 99.0 - - + +
653A GLN* 1.3 52.9 + - - +
655A LEU* 3.3 7.6 + - + +
656A ARG* 2.7 35.7 + - - +
674A PRO* 4.0 11.7 - - + -
688A TRP* 3.8 18.4 - - + +
689A GLN* 3.7 42.0 - - - +
690A ILE* 4.2 12.7 - - + +
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Residues in contact with GLN 653 (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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649A PRO 2.9 13.3 + - - +
650A LEU* 3.2 19.0 + - + +
652A LEU* 1.3 75.2 - - - +
654A GLN* 1.3 63.9 + - + +
656A ARG* 3.2 41.7 + - - +
657A ASN* 3.1 34.9 + - - +
674A PRO* 3.6 19.1 - - + +
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Residues in contact with GLN 654 (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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650A LEU* 3.0 22.6 + - - +
651A PHE* 3.6 6.5 - - - +
652A LEU 3.2 0.2 - - - -
653A GLN* 1.3 77.0 - - + +
655A LEU* 1.3 54.8 + - - +
657A ASN* 2.9 10.9 + - - +
658A LEU* 2.8 34.1 + - - +
714A LEU* 3.8 26.1 - - + +
715A PRO* 5.8 0.5 - - - +
716A GLU* 2.4 34.6 + - - +
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Residues in contact with LEU 655 (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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638A ILE* 4.1 27.4 - - + -
651A PHE* 3.2 26.4 + - + +
652A LEU* 3.7 9.9 - - + +
654A GLN* 1.3 74.4 - - - +
656A ARG* 1.3 57.7 + - - +
658A LEU* 4.2 4.7 - - + -
659A LEU* 2.7 62.5 + - + +
690A ILE* 5.8 3.1 - - + -
707A THR* 4.8 8.3 - - + -
708A LEU* 5.6 6.3 - - + -
711A ILE* 3.7 30.7 - - + -
714A LEU* 3.8 12.9 - - + +
722A TRP* 6.0 2.7 - - + -
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Residues in contact with ARG 656 (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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652A LEU 2.7 21.2 + - - +
653A GLN* 3.2 31.8 + - - +
655A LEU* 1.3 73.4 - - - +
657A ASN* 1.3 69.2 + - - +
659A LEU* 3.3 10.2 + - - +
660A GLN* 3.1 55.7 + - - +
671A VAL* 2.6 45.9 + - + +
672A LEU* 4.6 0.2 - - - +
673A GLY 3.0 26.6 + - - +
674A PRO* 4.7 1.0 - - + +
690A ILE* 3.7 21.7 - - + +
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Residues in contact with ASN 657 (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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653A GLN* 3.1 25.8 + - - +
654A GLN* 2.9 11.5 + - - +
656A ARG* 1.3 93.6 + - - +
658A LEU* 1.3 62.6 + - - +
660A GLN* 3.5 12.0 + - - +
661A ALA* 3.3 21.0 + - - +
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Residues in contact with LEU 658 (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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654A GLN 2.8 18.8 + - - +
655A LEU* 3.7 8.1 - - + +
657A ASN* 1.3 70.7 - - - +
659A LEU* 1.3 64.9 + - - +
661A ALA* 3.0 19.2 + - + +
662A SER* 3.5 7.3 + - - -
707A THR* 3.7 27.1 + - + +
710A LEU* 4.0 31.0 - - + +
711A ILE* 5.5 2.5 - - + -
713A THR* 4.1 12.1 - - + +
714A LEU* 4.8 16.6 - - + -
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Residues in contact with LEU 659 (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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638A ILE* 4.5 3.6 - - + -
655A LEU* 2.7 44.4 + - + +
656A ARG* 3.5 7.2 - - - +
658A LEU* 1.3 73.2 - - - +
660A GLN* 1.3 63.9 + - + +
662A SER* 3.0 23.0 + - - -
665A ALA* 4.4 2.4 - - - +
669A LEU* 4.5 3.9 - - + +
671A VAL* 4.4 9.0 - - + -
690A ILE* 5.4 1.6 - - + -
692A LEU* 3.4 38.1 - - + -
703A ILE* 4.2 13.3 - - + +
704A VAL* 3.9 25.8 - - + -
707A THR* 3.6 30.3 - - + +
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Residues in contact with GLN 660 (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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656A ARG* 3.1 37.5 + - - +
657A ASN* 3.9 12.4 - - - +
659A LEU* 1.3 75.0 - - - +
661A ALA* 1.3 57.9 + - - +
662A SER 3.1 4.8 + - - +
665A ALA* 3.3 22.2 - - - +
669A LEU* 4.8 12.4 + - + +
670A TRP* 5.7 0.4 - - - +
671A VAL* 3.6 32.2 + - + +
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Residues in contact with ALA 661 (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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657A ASN 3.3 11.5 + - - +
658A LEU* 3.0 19.7 + - + +
660A GLN* 1.3 74.3 - - - +
662A SER* 1.3 65.3 + - - +
663A PRO* 3.6 3.3 - - - +
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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