Contacts of the helix formed by residues 880 - 885 (chain C) in PDB entry 1XD2
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 SER 880 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ALA 5.2 4.0 - - - -
69B ASP* 3.9 15.3 - - - -
70B GLN 5.3 0.2 - - - +
73B ARG* 4.0 0.4 - - - -
836C GLU* 3.1 39.3 + - - +
876C SER 3.1 7.7 + - - -
877C ALA 2.9 17.3 + - - -
879C ASN* 1.3 79.4 - - - +
881C SER* 1.3 61.2 + - - +
882C PRO* 3.2 8.7 - - - +
883C VAL 3.7 4.2 + - - -
884C TYR* 2.9 30.1 + - - +
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Residues in contact with SER 881 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP* 3.1 18.4 + - - +
73B ARG* 4.1 6.7 - - - +
102B ARG* 3.8 20.0 - - - +
103B VAL* 3.3 26.0 - - - +
880C SER* 1.3 72.7 - - - +
882C PRO* 1.3 69.9 - - - +
884C TYR* 4.6 0.9 - - - +
885C ARG* 3.3 26.2 + - - +
1010C PHE* 3.8 18.9 - - - -
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Residues in contact with PRO 882 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP* 4.6 1.6 - - - +
836C GLU* 4.1 8.7 - - + +
840C VAL* 4.0 11.0 - - + -
880C SER* 3.2 17.3 - - - +
881C SER* 1.3 97.5 - - - +
883C VAL* 1.3 60.9 + - + +
885C ARG* 3.6 2.1 - - - +
886C LEU* 3.4 10.7 - - - +
1006C THR 4.9 2.5 - - - +
1009C LEU* 3.6 44.0 - - + +
1010C PHE* 4.0 9.0 - - + +
1013C SER* 2.7 32.2 + - - +
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Residues in contact with VAL 883 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836C GLU* 4.1 17.9 - - + -
839C ILE* 3.8 44.0 - - + -
840C VAL* 4.5 4.9 - - + -
852C VAL* 5.5 0.2 - - + -
877C ALA 3.3 22.4 - - - +
878C MET* 3.8 14.4 - - - +
880C SER* 3.4 7.0 + - - +
882C PRO* 1.3 78.6 - - + +
884C TYR* 1.3 67.6 + - - +
885C ARG 3.2 2.5 - - - -
886C LEU* 3.1 18.9 + - + +
890C PHE* 3.4 25.6 - - + -
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Residues in contact with TYR 884 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ARG* 3.4 52.7 - - - +
878C MET 3.3 11.3 + - - +
879C ASN* 3.9 21.1 - - - +
880C SER 2.9 24.2 + - - +
881C SER* 4.6 2.0 - - - +
883C VAL* 1.3 72.0 - - - +
885C ARG* 1.3 65.3 + - + +
886C LEU 3.4 1.2 + - - -
887C ASP* 4.1 8.5 - - - +
890C PHE* 4.6 8.9 - - - -
905C HIS* 6.4 0.4 - + - -
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Residues in contact with ARG 885 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881C SER 3.3 20.6 + - - +
882C PRO 3.6 1.8 - - - +
884C TYR* 1.3 81.6 - - + +
886C LEU* 1.3 60.6 + - - +
887C ASP* 2.9 22.6 + - - +
1010C PHE* 4.0 18.3 - - - -
1013C SER* 2.7 58.7 + - - +
1014C LEU* 3.7 21.5 - - - +
1017C GLU* 2.7 24.8 + - - +
1018C PRO 3.7 13.1 + - - -
1019C ARG* 3.9 12.5 - - - +
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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