Contacts of the helix formed by residues 670 - 680 (chain D) in PDB entry 6UZA
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 670 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1005A SBJ 6.3 0.9 - - - +
464C ARG 5.1 0.2 - - - -
465C PHE 3.3 18.2 - - - +
466C GLU* 3.8 21.8 + - + +
467C GLY* 4.4 2.8 + - - +
653D PHE* 4.2 3.3 - - - -
660D ILE* 5.0 4.3 - - - +
666D GLU* 5.8 0.2 + - - -
668D PHE 4.2 0.3 - - - -
669D THR* 1.3 83.2 + - - +
671D VAL* 1.3 64.8 + - - +
672D GLU* 3.3 22.2 - - + +
673D GLU* 3.7 19.6 - - - +
674D SER* 3.0 28.1 + - - -
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Residues in contact with VAL 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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465C PHE* 3.3 48.1 + - + +
649D MET* 4.3 22.1 - - + +
650D ILE* 6.5 0.9 - - + -
653D PHE* 4.0 21.1 - - + -
670D THR* 1.3 77.1 - - - +
672D GLU* 1.3 57.3 + - - +
674D SER* 3.8 5.5 - - - +
675D PHE* 2.9 28.0 + - + +
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Residues in contact with GLU 672 (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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702A ASN* 5.0 3.1 + - - +
1005A SBJ 3.0 48.9 + - - +
670D THR* 3.8 18.0 - - + +
671D VAL* 1.3 77.0 - - - +
673D GLU* 1.3 74.4 + - + +
675D PHE* 3.3 12.0 + - + +
676D LYS* 2.9 52.1 + - - +
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Residues in contact with GLU 673 (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 GLU* 3.0 39.6 - - + +
667D ALA* 4.6 1.0 - - - -
668D PHE 4.0 6.1 - - - +
669D THR* 4.4 1.1 - - - +
670D THR* 3.4 30.4 + - - +
671D VAL 3.3 0.2 - - - -
672D GLU* 1.3 88.8 - - + +
674D SER* 1.3 55.4 + - - +
676D LYS* 3.4 25.7 + - - +
677D THR* 2.4 39.8 + - - -
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Residues in contact with SER 674 (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 MET* 3.1 31.4 + - - +
653D PHE* 4.2 13.0 - - - -
668D PHE* 3.8 34.5 - - - +
670D THR 3.0 17.2 + - - -
671D VAL* 4.0 4.3 - - - -
673D GLU* 1.3 74.4 - - - +
675D PHE* 1.3 61.8 + - - +
678D LEU* 3.4 26.5 + - - +
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Residues in contact with PHE 675 (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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1005A SBJ 3.6 58.3 - - + -
645D PHE* 3.4 32.4 - + - -
649D MET* 3.7 18.8 - - - -
671D VAL* 2.9 19.3 + - + +
672D GLU* 3.5 12.6 - - + +
673D GLU 3.2 0.2 - - - -
674D SER* 1.3 77.9 - - - +
676D LYS* 1.3 61.4 + - - +
678D LEU 3.4 1.4 + - - -
679D PHE* 2.9 34.6 + + + +
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Residues in contact with LYS 676 (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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701A GLU* 5.7 0.2 + - - -
702A ASN* 5.4 1.8 + - - -
705A TYR* 4.4 29.6 + - + +
1005A SBJ 4.1 32.9 + - + -
672D GLU* 2.9 41.5 + - - +
673D GLU* 3.5 32.5 + - - +
675D PHE* 1.3 77.2 - - - +
677D THR* 1.3 65.0 + - - +
679D PHE* 4.2 7.0 - - - -
680D TRP* 2.9 49.2 + - + +
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Residues in contact with THR 677 (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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667D ALA* 3.4 28.6 - - + +
668D PHE* 3.7 31.2 - - + -
673D GLU* 2.4 24.8 + - - -
674D SER 4.4 0.2 - - - -
676D LYS* 1.3 78.2 - - - +
678D LEU* 1.3 60.5 + - - +
681D ALA* 3.4 12.6 + - - +
686D SER* 3.1 29.5 + - - +
690D SER* 3.9 14.6 - - - +
708D TYR* 4.1 3.2 + - - +
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Residues in contact with LEU 678 (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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645D PHE* 3.3 18.4 - - + +
648D PHE* 3.7 18.2 - - + +
649D MET* 3.5 37.0 - - + +
652D MET* 3.8 16.4 - - + -
668D PHE* 3.6 24.9 - - + -
674D SER 3.4 14.7 + - - +
675D PHE 3.4 1.2 + - - -
676D LYS 3.3 0.4 - - - -
677D THR* 1.3 75.7 - - - +
679D PHE* 1.3 64.3 + - - +
681D ALA* 3.8 3.0 + - - -
682D ILE* 3.7 4.3 - - - +
708D TYR* 4.1 6.1 - - + -
711D TYR* 2.5 52.7 + - + +
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Residues in contact with PHE 679 (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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709A GLY* 3.9 15.0 - - - -
713A VAL* 4.1 18.6 - - + -
1005A SBJ 3.8 52.5 - - + -
645D PHE* 3.4 14.5 - + + -
675D PHE* 2.9 30.9 + + + +
676D LYS* 3.3 7.2 + - - +
678D LEU* 1.3 77.5 - - - +
680D TRP* 1.3 75.2 + + - +
681D ALA 3.1 2.6 + - - -
682D ILE* 3.3 32.4 + - + +
683D PHE* 3.9 27.1 - + - -
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Residues in contact with TRP 680 (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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688A VAL* 3.8 27.8 - - + +
705A TYR* 4.0 26.0 - + - -
708A TYR* 3.5 29.6 - + + -
709A GLY* 3.6 23.1 - - - -
712A ASN* 3.7 22.7 - - - -
1005A SBJ 3.6 18.6 - - + +
676D LYS* 2.9 37.1 + - + +
679D PHE* 1.3 84.0 - + - +
681D ALA* 1.3 58.9 + - - +
682D ILE 3.3 0.7 - - - -
683D PHE* 3.7 17.0 + + - +
684D GLY 3.5 2.6 + - - -
685D LEU* 2.9 55.8 + - + +
686D SER* 3.7 13.0 - - - +
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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