Contacts of the strand formed by residues 1073 - 1077 (chain B) in PDB entry 6X34
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 ARG1073 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695B TYR* 2.9 36.4 + - - -
827B LYS* 4.7 13.1 - - - +
829B TYR* 4.8 11.0 - - - +
840B VAL 4.6 2.4 + - - -
841B GLY* 4.3 6.4 - - - -
842B PRO* 3.9 33.4 - - + +
1071B ARG 4.7 2.5 - - - +
1072B VAL* 1.3 79.7 - - - +
1074B ILE* 1.3 59.3 + - - +
1075B PHE* 3.8 30.5 + - + -
1193B SER* 3.3 7.1 - - - -
1194B LEU* 3.0 32.1 + - + +
1238B PHE* 4.3 6.5 - - - -
1239B SER* 3.0 35.2 + - - +
1241B SER* 3.1 23.5 + - - +
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Residues in contact with ILE1074 (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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1072B VAL* 4.2 2.6 + - + -
1073B ARG* 1.3 71.2 - - - +
1075B PHE* 1.3 62.0 + - - +
1076B ARG 3.3 5.2 + - - -
1109B LEU* 5.8 4.3 - - + -
1111B PRO* 5.3 13.7 - - + +
1115B LEU* 5.6 10.5 - - + -
1191B VAL* 5.0 8.3 - - + -
1192B CYS 3.4 6.3 - - - +
1193B SER* 4.6 2.0 - - - +
1238B PHE* 3.9 0.5 - - - -
1239B SER* 2.9 35.1 + - - +
1605B TRP* 4.6 11.7 - - + -
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Residues in contact with PHE1075 (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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829B TYR* 4.2 20.0 - + + -
839B LEU* 3.6 48.2 - - + -
840B VAL 4.4 4.9 - - - -
1073B ARG* 3.8 32.5 - - + -
1074B ILE* 1.3 69.2 - - - +
1076B ARG* 1.3 61.5 + - - +
1190B PRO 4.4 0.2 - - - +
1191B VAL* 3.3 3.3 - - - -
1192B CYS* 2.5 55.2 + - + +
1193B SER 4.8 0.4 - - - -
1194B LEU* 3.7 29.8 - - + -
1236B THR* 5.7 6.3 - - - -
1237B TRP 3.3 9.0 - - - +
1238B PHE* 3.6 26.9 - - + -
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Residues in contact with ARG1076 (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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1074B ILE* 3.3 4.3 + - + +
1075B PHE* 1.3 75.3 - - - +
1077B ALA* 1.3 65.9 + - - +
1109B LEU* 5.0 7.4 - - + -
1190B PRO 3.9 3.8 - - - +
1191B VAL* 3.9 18.4 - - + -
1236B THR* 4.1 4.3 - - - -
1237B TRP* 2.9 29.1 + - - +
1605B TRP* 3.6 34.1 - - + -
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Residues in contact with ALA1077 (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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1076B ARG* 1.3 80.4 - - - +
1078B GLU* 1.3 68.2 + - - +
1079B LYS* 3.6 1.9 + - - -
1081B TYR* 5.1 3.4 - - + +
1107B PRO* 6.1 1.4 - - - +
1189B LEU* 3.9 21.1 - - + +
1190B PRO* 3.6 24.5 + - + +
1226B PHE* 6.5 0.2 - - + -
1234B VAL* 6.0 4.3 - - + -
1235B THR 4.9 7.9 - - - +
1236B THR* 5.1 0.4 - - - +
1237B TRP* 3.5 13.9 - - - +
1605B TRP* 5.6 0.9 - - - -
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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