Contacts of the helix formed by residues 666 - 674 (chain D) in PDB entry 6VVT
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 666 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588D LEU 4.3 1.7 + - - -
589D THR 3.9 2.9 + - - -
590D THR 4.2 1.8 - - - +
591D LEU* 3.6 37.7 - - + -
629D VAL 3.7 10.0 + - - -
630D ARG* 4.3 2.7 - - - -
631D ALA 3.0 22.7 - - - +
633D ILE* 4.8 1.8 - - - -
665D THR* 1.3 85.2 + - - +
667D LEU* 1.3 65.1 + - - +
668D GLY* 3.6 2.8 + - - -
669D ARG* 3.0 38.0 + - - +
670D VAL* 2.9 18.8 + - - +
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Residues in contact with LEU 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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615D PRO* 4.7 9.4 - - + +
618D ALA* 3.6 47.8 - - + +
619D ILE* 4.0 7.2 - - + +
622D MET* 3.2 32.3 - - + -
627D LEU* 4.1 13.5 - - + -
628D SER 4.9 1.5 + - - +
629D VAL* 3.4 12.4 + - - +
631D ALA 4.5 0.8 + - - -
633D ILE* 4.5 11.2 - - + +
666D THR* 1.3 72.2 - - - +
668D GLY* 1.3 52.7 + - - +
670D VAL* 3.1 18.1 + - + -
671D MET* 2.7 52.7 + - + +
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Residues in contact with GLY 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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588D LEU* 3.1 45.3 - - - +
589D THR* 4.4 0.4 - - - -
629D VAL* 3.1 12.4 + - - +
666D THR* 3.1 1.2 - - - -
667D LEU* 1.3 75.8 - - - +
669D ARG* 1.3 50.8 + - - +
671D MET* 2.9 6.5 + - - -
672D PHE* 2.6 36.0 + - - +
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Residues in contact with ARG 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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588D LEU 4.0 1.0 + - - -
589D THR* 2.7 35.0 + - + +
591D LEU* 3.4 33.9 - - - +
665D THR* 4.5 5.9 - - - +
666D THR* 3.0 36.0 + - - +
668D GLY* 1.3 73.1 - - - +
670D VAL* 1.3 57.7 - - - +
672D PHE* 3.5 7.7 - - - +
673D ASN* 2.9 38.2 + - - +
682D PHE* 4.2 3.1 - - + -
684D ASN* 3.2 38.7 + - - +
685D GLU* 3.6 24.5 - - - +
686D GLN* 3.5 17.0 - - - +
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Residues in contact with VAL 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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615D PRO* 4.1 25.4 - - + -
633D ILE* 5.5 1.1 - - + -
635D VAL* 4.4 17.3 - - + -
637D LEU* 4.1 19.1 - - + -
665D THR* 3.1 25.6 - - + +
666D THR 2.9 12.5 + - - +
667D LEU* 3.3 16.2 - - + +
668D GLY 3.1 0.2 - - - -
669D ARG* 1.3 73.9 - - - +
671D MET* 1.3 64.9 + - + +
672D PHE 3.1 0.5 + - - -
673D ASN* 3.3 3.6 + - - +
674D GLU* 3.1 33.1 + - + +
682D PHE* 4.1 15.0 - - + -
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Residues in contact with MET 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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588D LEU* 3.7 13.7 - - + -
619D ILE* 5.2 14.1 - - + -
622D MET* 4.0 13.5 - - + +
629D VAL* 3.4 34.1 - - + -
667D LEU* 2.7 31.2 + - + +
668D GLY* 3.5 6.3 - - - +
670D VAL* 1.3 72.9 - - + +
672D PHE* 1.3 62.4 + - - +
674D GLU* 3.5 22.8 - - - +
675D LEU* 3.4 20.7 - - - +
722D TRP* 3.5 25.6 - - + +
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Residues in contact with PHE 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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585D LEU* 3.7 41.7 - - + -
588D LEU* 4.0 6.4 - - + +
589D THR* 3.7 22.9 - - + -
668D GLY 2.6 19.2 + - - +
669D ARG 3.5 4.9 - - - +
670D VAL 3.1 0.2 - - - -
671D MET* 1.3 71.4 - - - +
673D ASN* 1.3 67.3 + - - +
675D LEU* 2.6 42.0 + - + +
676D LEU* 3.3 27.4 - - + +
683D VAL* 5.5 1.1 - - + -
687D MET* 3.2 45.5 - - + -
692D GLN* 5.1 3.6 - - + -
695D ILE* 4.9 2.7 - - + -
715D LEU* 3.7 21.8 - - + -
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Residues in contact with ASN 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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640D LEU* 5.8 4.0 - - + -
669D ARG* 2.9 29.8 + - - +
670D VAL 3.3 2.2 + - - +
672D PHE* 1.3 81.2 - - - +
674D GLU* 1.3 61.3 + - - +
676D LEU* 3.1 31.8 + - - +
677D PRO 4.7 2.3 - - - +
680D TYR 5.3 0.7 - - - +
681D PRO 3.8 3.8 - - - +
682D PHE* 3.5 47.8 - - + -
683D VAL* 3.3 32.6 + - - +
684D ASN 4.1 5.3 - - - +
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Residues in contact with GLU 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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173B LYS* 3.6 25.5 + - - -
615D PRO* 4.1 24.1 - - - +
619D ILE* 5.9 2.3 - - - +
670D VAL* 3.1 21.9 + - + +
671D MET* 3.5 23.1 - - - +
672D PHE 3.0 0.6 + - - -
673D ASN* 1.3 76.2 - - - +
675D LEU* 1.3 66.9 + - + +
676D LEU 3.4 6.6 - - - +
714D LYS* 5.0 5.7 + - - -
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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