Contacts of the strand formed by residues 1073 - 1077 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695D TYR* 2.9 36.6 + - - -
827D LYS* 4.7 13.1 + - - +
829D TYR* 4.8 11.0 - - - +
840D VAL 4.6 2.4 + - - -
841D GLY* 4.3 6.6 - - - -
842D PRO* 3.9 33.3 - - + +
1071D ARG 4.7 2.2 - - - +
1072D VAL* 1.3 80.4 - - - +
1074D ILE* 1.3 60.2 + - - +
1075D PHE* 3.8 31.4 + - + -
1192D CYS 3.9 0.2 - - - +
1193D SER* 3.3 6.8 - - - -
1194D LEU* 3.0 31.1 + - + -
1238D PHE* 4.3 6.3 - - + -
1239D SER* 3.0 34.9 + - - +
1241D SER* 3.1 23.1 + - - +
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Residues in contact with ILE1074 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072D VAL* 4.2 3.0 + - + -
1073D ARG* 1.3 71.4 - - - +
1075D PHE* 1.3 61.4 + - - +
1076D ARG 3.3 6.2 + - - +
1109D LEU* 5.8 4.7 - - + -
1111D PRO* 5.3 13.0 - - + +
1115D LEU* 5.6 10.3 - - + -
1191D VAL* 5.0 8.7 - - + -
1192D CYS 3.4 5.8 - - - +
1193D SER* 4.6 2.2 - - - +
1238D PHE* 3.9 0.5 - - - -
1239D SER* 2.9 34.1 + - - +
1605D TRP* 4.6 11.3 - - + -
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Residues in contact with PHE1075 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829D TYR* 4.2 20.9 - + + -
839D LEU* 3.6 47.6 - - + -
840D VAL 4.4 4.9 - - - -
1073D ARG* 3.8 34.1 - - + -
1074D ILE* 1.3 69.9 - - - +
1076D ARG* 1.3 62.0 + - - +
1190D PRO 4.4 0.2 - - - +
1191D VAL* 3.3 3.4 - - - -
1192D CYS* 2.5 56.1 + - + +
1193D SER 4.8 0.4 - - - -
1194D LEU* 3.7 29.2 - - + -
1236D THR* 5.7 5.8 - - - -
1237D TRP 3.3 8.7 - - - +
1238D PHE* 3.6 26.5 - + + -
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Residues in contact with ARG1076 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074D ILE* 3.3 4.3 + - + +
1075D PHE* 1.3 76.6 - - - +
1077D ALA* 1.3 67.1 + - - +
1109D LEU* 5.0 8.5 - - + -
1190D PRO 3.9 4.3 - - - +
1191D VAL* 3.9 17.3 - - + -
1236D THR* 4.1 4.2 - - - -
1237D TRP* 2.9 29.5 + - - +
1605D TRP* 3.6 33.7 - - + -
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Residues in contact with ALA1077 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076D ARG* 1.3 81.3 - - - +
1078D GLU* 1.3 67.7 + - - +
1079D LYS* 3.6 1.7 + - - -
1081D TYR* 5.1 3.4 - - + +
1107D PRO* 6.1 1.2 - - - +
1189D LEU* 3.9 20.2 - - + +
1190D PRO* 3.6 24.1 + - + +
1234D VAL* 6.0 4.3 - - + -
1235D THR 4.9 8.1 - - - +
1236D THR* 5.1 0.2 - - - +
1237D TRP* 3.5 13.2 - - - +
1605D 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