Contacts of the helix formed by residues 668 - 675 (chain D) in PDB entry 5UHE
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 LEU 668 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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615D PRO* 4.3 9.2 - - + +
618D ALA* 3.5 42.6 - - + +
619D ILE* 4.2 22.7 - - + +
622D ALA* 4.6 9.0 - - + -
627D LEU* 3.9 19.5 - - + -
628D SER 4.9 0.4 - - - +
629D VAL* 3.9 25.6 + - + -
631D ALA 4.4 1.8 + - - -
633D ILE* 4.2 12.1 - - + +
635D VAL* 6.1 1.3 - - + -
667D THR* 1.3 71.3 - - - +
669D GLY* 1.3 56.5 + - - +
671D VAL* 3.1 30.6 + - + +
672D MET* 3.1 22.4 + - + +
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Residues in contact with GLY 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* 3.3 31.3 - - - +
629D VAL* 3.2 31.5 + - - +
667D THR 3.1 1.0 - - - -
668D LEU* 1.3 74.8 - - - +
670D ARG* 1.3 63.6 + - - +
671D VAL 3.1 1.3 - - - -
672D MET* 3.4 8.8 + - - +
673D PHE 3.2 17.0 + - - -
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Residues in contact with ARG 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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588D LEU 4.1 0.4 + - - -
589D THR* 3.0 49.2 + - + -
591D GLU* 3.4 45.4 + - - +
666D THR* 4.3 6.8 - - - +
667D THR* 3.0 32.7 + - - +
669D GLY* 1.3 75.7 - - - +
671D VAL* 1.3 59.4 + - - +
673D PHE* 3.3 8.7 - - - +
674D ASN* 3.0 25.1 + - - -
683D PHE* 4.1 8.1 - - + -
684D VAL 4.9 3.1 - - - +
685D ASN* 2.7 42.0 + - - +
686D LYS* 3.1 28.9 + - - +
687D GLN* 3.7 5.1 - - - +
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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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615D PRO* 4.5 12.3 - - + -
635D VAL* 5.7 8.1 - - + -
637D LEU* 4.2 30.3 - - + -
640D LEU* 4.1 9.5 - - + +
666D THR* 3.6 21.1 - - - +
667D THR 3.2 5.6 + - - +
668D LEU* 3.1 18.9 + - + +
670D ARG* 1.3 73.3 - - - +
672D MET* 1.3 67.1 + - + +
673D PHE 3.0 2.7 + - - -
674D ASN* 3.1 12.3 + - - +
675D GLU* 3.2 25.5 + - - +
683D PHE* 4.1 14.4 - - + -
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Residues in contact with MET 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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588D LEU* 5.6 4.9 - - + -
619D ILE* 5.3 16.4 - - + -
629D VAL* 4.7 11.7 - - - -
668D LEU* 3.1 25.3 + - + +
669D GLY* 3.4 8.7 + - - +
671D VAL* 1.3 78.1 - - + +
673D PHE* 1.3 61.5 + - - +
675D GLU* 3.4 24.5 + - - +
676D LEU* 3.2 23.7 - - - +
723D TRP* 4.5 30.1 - - + +
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Residues in contact with PHE 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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585D LEU* 4.5 19.1 - - + -
588D LEU* 4.3 5.6 - - + +
589D THR* 4.2 13.0 - - + -
669D GLY 3.2 12.5 + - - +
670D ARG* 3.3 11.0 - - - +
671D VAL 3.0 0.4 - - - -
672D MET* 1.3 78.6 - - - +
674D ASN* 1.3 72.6 + - - +
675D GLU 3.2 0.2 - - - -
676D LEU* 3.2 34.1 - - + +
677D LEU* 4.2 13.1 - - + +
684D VAL* 4.0 14.1 - - + -
688D MET* 3.4 47.1 - - + -
693D GLN* 5.4 3.8 - - + -
696D ILE* 3.9 14.6 - - + -
716D LEU* 3.7 24.9 - - + -
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Residues in contact with ASN 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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640D LEU* 3.3 13.5 - - + +
670D ARG 3.0 21.0 + - - -
671D VAL 3.1 1.8 + - - +
673D PHE* 1.3 78.5 - - - +
675D GLU* 1.3 57.4 + - - +
676D LEU 2.9 9.6 + - - -
677D LEU* 3.5 20.7 + - - +
678D PRO 3.2 21.5 - - - +
681D TYR 5.0 1.6 - - - +
682D PRO 4.2 0.5 - - - +
683D PHE* 3.3 46.8 - - + -
684D VAL* 3.1 43.8 + - - +
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Residues in contact with GLU 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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615D PRO* 4.6 13.3 - - - +
619D ILE* 6.0 1.7 - - - +
640D LEU* 4.3 16.4 - - + -
671D VAL* 3.2 26.1 + - + +
672D MET* 3.4 30.2 - - - +
673D PHE 3.2 1.0 - - - -
674D ASN* 1.3 76.9 - - - +
676D LEU* 1.3 65.5 + - + +
677D LEU 3.6 0.2 - - - -
678D PRO* 3.7 13.6 - - - +
679D LEU* 5.8 2.0 - - - +
715D LYS* 5.4 3.5 + - - +
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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