Contacts of the strand formed by residues 1038 - 1042 (chain A) in PDB entry 6Q6Q
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 VAL1038 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030A VAL* 3.6 22.9 - - + -
1031A HIS 3.2 11.2 - - - +
1032A ILE* 3.7 20.2 - - + -
1033A TYR* 5.1 0.9 - - - -
1036A GLY 4.0 2.5 - - - +
1037A SER* 1.3 82.6 - - - +
1039A LEU* 1.3 63.6 + - - +
1040A VAL* 4.2 1.1 - - + +
1059A VAL* 4.3 8.5 - - + -
1063A LEU* 4.4 2.0 - - + -
1065A MET* 3.7 32.8 - - + -
1069A ASN* 3.1 9.1 + - - +
1070A VAL* 3.5 19.9 - - + +
1071A HIS* 2.9 28.8 + - - +
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Residues in contact with LEU1039 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029A LEU 3.8 1.0 - - - +
1030A VAL* 3.4 1.6 - - - -
1031A HIS* 2.8 49.1 + - + +
1033A TYR* 3.7 34.8 - - + +
1038A VAL* 1.3 74.6 - - - +
1040A VAL* 1.3 64.3 + - - +
1041A THR* 5.7 2.9 - - + +
1071A HIS* 3.3 38.8 - - + +
1072A LEU* 4.3 2.2 - - - -
1073A ARG* 4.1 23.3 - - + +
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Residues in contact with VAL1040 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028A ALA* 5.2 0.2 - - + -
1029A LEU 3.4 3.6 - - - +
1030A VAL* 3.7 26.2 - - + +
1038A VAL* 5.0 0.4 - - + -
1039A LEU* 1.3 78.1 - - - +
1041A THR* 1.3 73.3 + - - +
1042A HIS* 5.1 0.7 - - + -
1055A MET* 5.5 2.0 - - + -
1056A ILE* 3.7 29.8 - - + -
1059A VAL* 4.3 7.9 - - + -
1070A VAL* 3.9 9.6 - - + -
1071A HIS 3.1 7.1 + - - +
1072A LEU* 3.2 30.6 - - + +
1073A ARG 4.6 1.2 + - - -
1099A VAL* 4.1 27.4 - - + -
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Residues in contact with THR1041 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028A ALA* 3.3 4.2 - - - +
1029A LEU* 2.8 59.3 + - + +
1039A LEU* 5.7 3.1 - - + +
1040A VAL* 1.3 78.0 - - - +
1042A HIS* 1.3 69.9 + - - +
1072A LEU* 4.3 6.3 - - - -
1073A ARG 6.2 0.4 - - - -
1074A GLY 3.2 20.1 + - - -
1075A THR* 4.5 1.6 - - - -
1076A SER 4.8 0.2 + - - -
1079A THR* 3.8 31.6 + - + -
1080A VAL* 3.9 3.8 - - + +
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Residues in contact with HIS1042 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027A ALA 3.6 15.7 - - - +
1028A ALA* 4.0 8.1 - - + -
1040A VAL* 5.1 0.9 - - + -
1041A THR* 1.3 81.3 + - - +
1043A GLY* 1.3 61.5 + - - +
1044A GLY* 2.9 28.9 + - - -
1051A VAL* 3.6 23.1 - - + -
1052A HIS* 3.0 38.3 + + - -
1055A MET* 3.3 28.7 - - + +
1072A LEU* 3.7 15.8 - - + +
1074A GLY 4.6 1.1 + - - +
1075A THR* 3.3 21.3 + - - +
1076A SER 5.1 0.2 + - - -
1080A VAL* 3.8 9.7 - - - +
1095A ASN* 3.7 12.4 + - + +
1099A VAL* 4.3 7.9 - - + -
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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