Contacts of the helix formed by residues 660 - 671 (chain D) in PDB entry 1EQQ
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 PHE 660 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623D MET* 4.2 12.3 - - + -
628D ALA 3.6 4.0 - - - -
629D VAL* 3.4 37.7 - - + -
658D VAL* 3.6 15.0 - - + -
659D LEU* 1.3 80.0 - - - +
661D GLY* 1.3 73.3 + - - +
662D LYS 3.4 0.2 + - - -
663D LEU* 3.4 13.2 + - - +
664D ALA* 3.0 9.6 + - - -
684D ARG* 3.8 16.8 - - - -
701D VAL* 3.5 26.9 - - + -
702D VAL 4.1 18.8 + - - +
703D VAL* 4.4 17.0 - - + -
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Residues in contact with GLY 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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623D MET* 6.0 0.4 - - - +
627D GLY* 5.6 3.0 - - - -
628D ALA* 3.3 17.3 + - - +
660D PHE* 1.3 78.8 - - - +
662D LYS* 1.3 66.6 + - - +
664D ALA* 2.9 15.8 + - - +
665D GLU* 3.2 10.7 + - - +
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Residues in contact with LYS 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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660D PHE 3.4 0.4 + - - -
661D GLY* 1.3 68.4 - - - -
663D LEU* 1.3 75.2 + - + +
665D GLU* 2.5 43.1 + - - +
666D VAL* 2.6 31.9 + - + +
715D ARG* 5.6 7.5 - - - +
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Residues in contact with LEU 663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659D LEU* 3.9 14.5 - - + +
660D PHE 3.4 10.0 + - - +
662D LYS* 1.3 98.4 - - + +
664D ALA* 1.3 65.1 + - - +
666D VAL* 3.4 12.7 - - + +
667D ALA* 2.7 27.0 + - - +
702D VAL* 5.7 5.8 - - + +
707D GLY* 4.9 7.0 - - - -
708D THR* 3.0 50.0 - - + +
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Residues in contact with ALA 664 (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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620D VAL* 5.1 2.0 - - + +
628D ALA* 3.2 31.4 - - + +
630D ALA* 3.5 33.2 - - - +
659D LEU* 3.7 4.1 - - - +
660D PHE* 3.0 13.9 + - - -
661D GLY 2.9 15.5 + - - +
663D LEU* 1.3 78.0 - - - +
665D GLU* 1.3 59.6 + - - +
667D ALA* 3.2 4.2 - - - +
668D SER* 3.0 18.8 + - - -
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Residues in contact with GLU 665 (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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620D VAL* 5.7 0.7 - - - -
622D TYR* 4.7 14.3 + - - +
628D ALA* 4.1 17.5 - - + +
661D GLY 3.7 10.1 - - - +
662D LYS* 2.5 24.8 + - - +
664D ALA* 1.3 70.0 - - - +
666D VAL* 1.3 68.3 + - + +
668D SER* 2.7 20.1 + - - -
669D GLU* 2.8 29.0 + - + +
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Residues in contact with VAL 666 (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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662D LYS* 2.6 49.1 + - + +
663D LEU* 3.4 16.6 - - + +
665D GLU* 1.3 73.3 - - + +
667D ALA* 1.3 66.3 + - - +
669D GLU* 3.0 6.5 + - - +
670D TYR* 2.9 36.5 + - + +
671D LEU* 4.8 0.2 - - - +
708D THR* 5.5 4.5 - - + -
710D GLN* 4.8 12.6 - - - +
715D ARG* 4.7 24.0 - - + +
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Residues in contact with ALA 667 (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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618D PRO* 3.8 2.6 - - + +
630D ALA* 3.9 6.3 - - + -
632D ILE* 4.5 2.9 - - + -
659D LEU* 3.2 28.9 - - + -
663D LEU 2.7 8.9 + - - +
664D ALA 3.2 8.1 - - - +
666D VAL* 1.3 71.3 - - - +
668D SER* 1.3 60.1 + - - +
671D LEU* 2.6 69.1 + - + +
708D THR* 5.8 1.9 - - + +
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Residues in contact with SER 668 (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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618D PRO* 4.6 6.7 - - - +
620D VAL* 3.1 38.0 - - - +
622D TYR* 5.5 1.8 + - - -
664D ALA 3.0 6.5 + - - -
665D GLU* 2.7 18.8 + - - -
667D ALA* 1.3 77.0 - - - +
669D GLU* 1.3 63.0 + - - +
672D ARG* 3.1 25.6 + - - +
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Residues in contact with GLU 669 (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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665D GLU* 2.8 30.5 + - - +
666D VAL* 3.9 2.2 - - - +
668D SER* 1.3 77.2 - - - +
670D TYR* 1.3 105.4 + - + +
672D ARG* 3.5 9.0 + - - -
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Residues in contact with TYR 670 (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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666D VAL* 2.9 24.8 + - + +
669D GLU* 1.3 122.9 + - + +
671D LEU* 1.3 69.4 + - - +
672D ARG* 3.9 9.8 + - - +
675D SER* 4.3 4.3 + - - -
710D GLN* 4.3 23.6 + - - +
714D GLY 5.1 7.6 - - - +
715D ARG* 4.9 22.9 - - + -
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Residues in contact with LEU 671 (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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614D LEU* 3.9 17.3 - - + -
618D PRO* 2.9 18.3 - - + +
632D ILE* 4.1 15.7 - - + -
659D LEU* 4.4 2.7 - - + -
666D VAL* 4.8 0.7 - - + +
667D ALA* 2.6 52.3 + - + +
670D TYR* 1.3 74.6 - - - +
672D ARG* 1.3 87.0 + - - +
675D SER* 4.0 16.6 - - - -
677D VAL* 3.7 28.0 - - + -
708D THR* 5.1 6.1 - - + +
710D GLN* 4.0 17.9 - - - +
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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