Contacts of the strand formed by residues 1037 - 1042 (chain A) in PDB entry 4UI2
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 VAL1037 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1023A ILE 3.5 1.4 - - - +
1024A TYR* 3.2 8.3 - - - +
1025A TYR* 2.9 82.0 + - + +
1026A SER* 5.9 0.2 - - - -
1035A ASP 5.5 0.9 - - - +
1036A TRP* 1.3 71.9 - - - +
1038A ILE* 1.3 71.0 + - - +
1039A GLU* 5.2 2.7 - - - +
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Residues in contact with ILE1038 (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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1022A ILE* 3.9 18.8 - - + -
1023A ILE 3.6 2.9 - - - -
1024A TYR* 3.5 27.1 - - + -
1033A ILE 4.6 3.8 - - - +
1034A HIS* 4.0 16.4 - - - +
1036A TRP 3.1 24.5 - - - +
1037A VAL* 1.3 81.2 - - - +
1039A GLU* 1.3 63.5 + - - +
1040A PRO* 3.9 14.7 - - + +
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Residues in contact with GLU1039 (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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1022A ILE* 3.6 2.8 - - - -
1023A ILE* 2.8 49.5 + - + +
1025A TYR* 4.2 24.5 + - + -
1037A VAL* 5.2 1.7 - - - +
1038A ILE* 1.3 74.3 - - - +
1040A PRO* 1.3 75.5 - - + +
1041A VAL* 3.7 4.0 - - + +
1048A HIS* 3.1 33.2 + - + +
1049A GLN 4.2 4.5 - - - +
1050A ILE* 4.3 12.5 - - + +
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Residues in contact with PRO1040 (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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1021A TYR 3.8 5.8 - - - +
1022A ILE* 4.1 14.8 - - + -
1038A ILE* 3.9 15.2 - - + +
1039A GLU* 1.3 93.9 - - + +
1041A VAL* 1.3 65.6 + - - +
1048A HIS* 4.9 2.9 + - - -
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Residues in contact with VAL1041 (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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1008A TRP* 4.0 26.7 - - + -
1019A THR 4.8 0.2 - - - +
1020A GLY* 3.3 5.0 - - - -
1021A TYR* 3.0 36.5 + - + +
1023A ILE* 3.6 28.9 - - + -
1039A GLU 3.7 5.4 - - - +
1040A PRO* 1.3 81.9 - - - +
1042A VAL* 1.3 76.6 + - + +
1045A ARG* 4.5 5.4 - - + +
1048A HIS* 4.0 25.6 - - + +
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Residues in contact with VAL1042 (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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1019A THR 4.8 2.0 - - - -
1020A GLY* 4.4 0.7 - - - -
1021A TYR* 3.7 6.6 - - - -
1041A VAL* 1.3 93.3 - - + +
1043A GLY* 1.3 63.1 + - - +
1044A ASN* 3.4 27.3 + - - +
1045A ARG* 3.7 30.7 + - + -
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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