Contacts of the strand formed by residues 832 - 841 (chain C) in PDB entry 3IYD
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 HIS 832 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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762C ASN* 3.2 64.0 + - + +
763C THR 4.6 0.9 - - - +
830C THR* 3.6 3.6 + - + -
831C ILE* 1.3 72.3 - - - +
833C ILE* 1.3 92.0 + - - +
834C GLN* 3.0 35.9 + - + -
1056C VAL* 2.8 19.1 + - + +
1058C ARG* 3.7 43.8 + - + -
1239C VAL* 4.9 13.0 - - + -
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Residues in contact with ILE 833 (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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756C TYR* 4.8 13.0 - - + -
757C THR 4.1 17.3 - - - +
758C ARG* 3.5 31.4 + - - +
762C ASN* 3.7 8.3 - - - +
763C THR 4.9 7.9 - - - +
764C CYS* 6.2 1.1 - - - -
831C ILE* 3.4 28.3 - - + +
832C HIS* 1.3 100.7 - - - +
834C GLN* 1.3 68.8 + - - +
929C ILE* 3.6 30.7 - - + -
1053C TYR* 4.8 1.1 - - + -
1054C LEU 3.3 11.6 + - - +
1055C ALA* 3.6 14.8 - - + +
1056C VAL* 3.6 7.3 - - - +
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Residues in contact with GLN 834 (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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758C ARG* 3.2 25.2 + - - +
762C ASN* 5.3 1.6 + - - -
832C HIS* 3.0 35.6 + - + -
833C ILE* 1.3 78.0 - - - +
835C GLU* 1.3 70.4 + - - +
836C LEU* 4.5 5.4 - - + -
924C VAL 6.0 0.7 - - - +
1053C TYR* 4.6 0.5 - - - -
1054C LEU* 2.8 40.5 + - + +
1056C VAL* 4.9 5.1 - - + +
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Residues in contact with GLU 835 (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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758C ARG* 3.2 21.0 + - - +
834C GLN* 1.3 83.3 + - - +
836C LEU* 1.3 79.7 + - - +
837C ALA* 5.1 3.3 - - + +
1051C LYS* 4.3 21.3 - - - +
1052C VAL 4.4 3.5 + - - +
1053C TYR* 3.4 34.9 - - - +
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Residues in contact with LEU 836 (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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834C GLN* 4.5 4.0 - - + -
835C GLU* 1.3 89.6 - - - +
837C ALA* 1.3 64.2 + - - +
838C CYS* 6.5 0.4 - - - -
883C LEU* 4.7 19.1 - - + -
918C LEU* 4.4 23.3 - - + -
920C VAL* 5.3 4.0 - - + -
921C PRO* 4.5 20.4 - - + -
1052C VAL* 2.8 45.1 + - + +
1053C TYR 5.0 0.2 - - - +
1054C LEU* 3.6 39.0 - - + -
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Residues in contact with ALA 837 (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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835C GLU* 5.1 4.0 - - + +
836C LEU* 1.3 79.1 - - - +
838C CYS* 1.3 66.6 + - - +
839C VAL* 4.2 5.8 + - + +
918C LEU* 3.3 17.9 - - - +
1049C ILE* 4.5 12.6 - - + -
1050C VAL 3.4 12.1 - - - +
1051C LYS* 4.4 10.1 - - + -
1052C VAL* 4.5 1.3 - - - +
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Residues in contact with CYS 838 (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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837C ALA* 1.3 77.4 - - - +
839C VAL* 1.3 62.2 + - - +
840C SER 4.1 1.0 + - - -
850C ILE* 6.4 0.4 - - + -
883C LEU* 5.5 3.4 - - - -
884C VAL* 3.8 41.1 - - + -
886C LYS* 5.0 12.3 - - + -
918C LEU* 3.7 35.7 - - - -
1048C LYS 4.6 0.7 - - - +
1049C ILE* 3.4 2.9 - - - +
1050C VAL* 3.0 37.3 + - + +
1052C VAL* 5.9 1.6 - - - -
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Residues in contact with VAL 839 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837C ALA* 4.2 5.6 + - + +
838C CYS* 1.3 76.0 - - - +
840C SER* 1.3 74.1 + - - +
841C ARG* 3.9 20.5 + - + +
848C GLU* 5.1 0.3 - - - +
886C LYS* 4.9 8.6 - - - -
1043C ALA* 5.9 0.4 - - + -
1046C VAL* 3.7 25.1 - - + -
1048C LYS 4.7 0.9 - - - -
1049C ILE* 3.6 22.9 - - + -
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Residues in contact with SER 840 (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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838C CYS 4.1 1.2 + - - -
839C VAL* 1.3 73.9 - - - +
841C ARG* 1.3 61.7 + - - +
848C GLU* 3.4 26.5 + - - +
850C ILE* 4.7 8.3 - - - -
886C LYS* 5.0 3.3 - - - +
1046C VAL* 3.2 30.7 - - - +
1047C LEU* 3.2 23.0 - - - +
1048C LYS* 3.8 35.4 + - - -
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Residues in contact with ARG 841 (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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839C VAL* 4.1 19.9 + - + +
840C SER* 1.3 79.7 - - - +
842C ASP* 1.3 67.0 + - - +
843C THR* 3.4 10.5 + - - +
847C PRO* 3.9 4.0 - - - +
848C GLU* 2.8 29.3 + - - +
1045C GLY 3.2 9.4 - - - +
1046C VAL* 5.1 2.2 - - + -
1047C LEU* 3.9 5.4 - - - +
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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