Contacts of the strand formed by residues 1080 - 1083 (chain B) in PDB entry 4E70
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 PHE1080 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032B ALA* 5.0 2.5 - - + -
1037B ILE* 3.8 26.0 - - + -
1038B ALA* 3.8 34.1 - - + -
1041B ILE* 3.9 10.3 - - + -
1071B MET* 3.7 21.8 - - + -
1074B LEU* 3.7 34.5 + - + -
1075B VAL* 3.4 34.2 - - + +
1078B GLY 4.6 0.3 - - - -
1079B TYR* 1.3 98.9 + - + +
1081B THR* 1.3 70.2 + - - +
1099B TRP 3.2 15.5 - - - +
1100B LEU* 3.9 11.4 - - + -
1101B ALA* 3.9 5.1 - - - +
1104B SER* 4.1 3.4 - - - -
1107B LEU* 4.4 7.9 - - + -
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Residues in contact with THR1081 (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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1075B VAL* 4.0 7.6 - - - -
1080B PHE* 1.3 78.4 - - - +
1082B GLN* 1.3 64.8 + - - +
1098B TYR* 3.3 9.5 - - - +
1099B TRP* 2.9 49.7 + - + +
1100B LEU 4.5 3.5 + - - +
1101B ALA* 4.0 19.5 - - + -
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Residues in contact with GLN1082 (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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1068B SER 4.9 0.5 - - - +
1072B ARG* 3.7 35.4 + - - +
1075B VAL* 3.7 18.3 - - + +
1081B THR* 1.3 79.0 - - - +
1083B VAL* 1.3 64.2 + - - +
1084B ILE* 5.9 4.8 - - - +
1096B PRO* 4.4 15.3 - - + +
1097B SER 3.3 5.4 - - - +
1098B TYR* 3.6 31.6 + - + -
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Residues in contact with VAL1083 (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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1047B PRO* 5.2 9.2 - - + -
1082B GLN* 1.3 76.0 - - - +
1084B ILE* 1.3 72.0 + - - +
1085B THR* 4.9 8.3 - - - +
1096B PRO* 3.2 4.2 - - - +
1097B SER* 2.8 50.0 + - - +
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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