Contacts of the strand formed by residues 942 - 947 (chain B) in PDB entry 3I8E
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 PHE 942 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881B LEU* 3.8 29.4 - - + -
888B VAL* 4.4 13.5 - - + -
890B LEU* 4.3 7.2 - - + -
903B CYS* 3.7 26.9 - - - +
904B ASN 4.1 11.9 - - - +
905B HIS* 4.0 26.9 - - + +
922B LEU* 3.9 28.5 - - + -
933B LEU* 4.0 17.9 - - + -
934B ALA 3.3 17.5 - - - -
935B TYR* 4.1 15.9 - + + -
936B LYS* 5.1 0.7 - - - -
938B MET* 6.0 0.5 - - - +
941B ASN* 1.3 93.9 + - - +
943B GLU* 1.3 61.8 + - - +
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Residues in contact with GLU 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933B LEU* 4.5 2.5 - - - -
934B ALA* 3.3 31.0 + - - +
936B LYS* 3.0 39.2 + - + +
938B MET* 6.0 1.8 - - + -
942B PHE* 1.3 77.9 - - - +
944B GLU* 1.3 62.9 + - - +
945B ILE* 3.0 19.6 + - - +
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Residues in contact with GLU 944 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905B HIS* 4.1 7.8 + - + +
907B ASN* 3.6 28.5 - - - +
931B LEU* 4.2 11.2 - - + +
932B LEU 3.8 6.1 - - - +
933B LEU* 3.8 22.4 - - + +
943B GLU* 1.3 72.1 - - - +
945B ILE* 1.3 68.4 + - - +
946B ALA 4.6 6.5 - - - +
947B ARG* 3.8 21.7 + - - +
990B GLN* 3.5 31.7 + - - +
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Residues in contact with ILE 945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921B ILE* 4.6 12.6 - - + -
932B LEU* 3.0 37.1 + - + +
934B ALA* 3.7 28.9 - - + +
943B GLU* 3.0 26.1 + - - +
944B GLU* 1.3 72.9 - - - +
946B ALA* 1.3 67.5 + - + +
979B LYS* 4.0 14.8 - - + +
989B ARG* 4.2 14.3 - - + +
990B GLN* 3.6 16.8 - - - +
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Residues in contact with ALA 946 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931B LEU* 3.6 0.7 - - - +
932B LEU* 2.5 40.4 + - + +
944B GLU* 3.5 5.3 - - - +
945B ILE* 1.3 88.7 - - + +
947B ARG* 1.3 58.4 + - - +
979B LYS* 5.0 5.4 - - + -
989B ARG 3.8 12.8 - - - +
990B GLN* 3.3 16.6 - - - +
992B LEU* 3.8 25.6 - - + -
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Residues in contact with ARG 947 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907B ASN* 3.6 16.2 + - - -
928B ARG* 3.0 73.8 + - - +
930B VAL 3.5 12.3 + - - +
931B LEU* 4.0 23.1 - - + +
944B GLU* 3.8 19.3 + - - +
946B ALA* 1.3 75.1 - - - +
948B ASP* 1.3 69.2 + - - +
949B PHE* 3.3 41.7 - - + +
990B GLN* 3.2 6.6 + - - +
992B LEU* 3.1 28.1 + - - -
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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