Contacts of the strand formed by residues 1025 - 1032 (chain A) in PDB entry 3I7L
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 GLN1025 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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961A ASP* 5.3 8.5 + - - +
1024A THR* 1.3 75.3 - - - +
1026A GLY* 1.3 63.9 + - - +
1041A THR* 3.0 1.4 - - - +
1042A SER* 2.8 61.2 + - - +
1043A LEU* 5.6 2.8 + - - -
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Residues in contact with GLY1026 (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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1009A HIS* 6.2 0.4 - - - -
1024A THR 4.3 0.6 + - - -
1025A GLN* 1.3 74.7 - - - +
1027A SER* 1.3 62.1 + - - -
1028A VAL 4.3 0.4 - - - -
1040A VAL 4.5 2.5 - - - -
1041A THR* 2.7 31.4 - - - +
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Residues in contact with SER1027 (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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1009A HIS* 3.5 11.1 + - - +
1010A GLY* 2.8 44.8 + - - -
1011A SER* 3.2 23.5 + - - -
1026A GLY* 1.3 75.0 - - - -
1028A VAL* 1.3 64.0 + - - +
1029A LEU* 5.0 0.3 - - - +
1039A LEU* 3.4 16.8 - - - +
1040A VAL 3.8 2.9 - - - -
1139A ILE 5.2 0.2 + - - -
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Residues in contact with VAL1028 (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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958A GLU* 4.1 12.3 - - + -
960A LEU* 4.5 11.9 - - + -
966A LEU* 4.8 4.9 - - + -
1007A PHE* 3.8 30.3 - - + -
1008A CYS 4.0 3.8 - - - +
1009A HIS* 3.2 43.5 - - + +
1027A SER* 1.3 71.9 - - - +
1029A LEU* 1.3 72.2 + - - +
1030A PHE* 4.4 0.5 - - - -
1039A LEU* 3.4 5.7 - - - +
1040A VAL* 2.9 49.9 + - + +
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Residues in contact with LEU1029 (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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9A ALA* 5.3 3.6 - - + -
362A MET* 5.1 4.5 - - - -
364A VAL* 3.9 19.5 - - + -
375A LEU* 4.5 14.6 - - + -
1006A VAL 3.9 0.2 - - - +
1007A PHE* 3.3 4.7 - - - -
1008A CYS* 2.9 38.6 + - - +
1010A GLY* 3.1 34.5 - - - +
1011A SER* 3.7 11.2 - - - +
1012A LEU* 4.3 22.7 - - + +
1027A SER* 4.1 2.8 - - - +
1028A VAL* 1.3 75.8 - - - +
1030A PHE* 1.3 59.4 + - - +
1037A ILE* 4.2 16.2 - - + -
1038A GLY 3.5 14.6 - - - +
1039A LEU* 4.8 10.5 - - + -
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Residues in contact with PHE1030 (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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6A VAL* 5.3 4.9 - - + -
7A VAL 5.1 0.4 - - - -
362A MET* 4.3 6.4 - - - -
974A LEU* 5.2 4.7 - - + -
1000A LEU* 3.6 35.7 - - + -
1004A VAL* 3.6 19.7 - - + -
1006A VAL 3.1 12.1 - - - +
1007A PHE* 3.6 21.5 - + + -
1028A VAL 4.4 0.9 - - - -
1029A LEU* 1.3 78.4 - - - +
1031A GLY* 1.3 58.3 + - - +
1032A THR* 3.7 16.8 - - + -
1036A MET* 3.8 16.2 - - + -
1037A ILE* 3.4 5.9 - - - +
1038A GLY* 2.9 70.3 + - - -
1039A LEU* 3.4 6.1 - - - -
1040A VAL* 4.1 24.7 - - + -
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Residues in contact with GLY1031 (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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359A ILE* 4.2 10.1 - - - -
362A MET* 3.4 26.2 - - - +
1004A VAL* 3.7 3.5 - - - +
1005A ASN* 2.9 25.1 + - - +
1006A VAL* 3.0 13.2 + - - +
1030A PHE* 1.3 73.2 - - - +
1032A THR* 1.3 62.5 + - - -
1036A MET 3.6 5.4 - - - -
1037A ILE* 4.8 0.2 - - - -
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Residues in contact with THR1032 (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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359A ILE* 3.3 21.0 + - - +
1002A GLU* 3.8 20.6 - - + -
1003A PHE 3.1 15.0 - - - +
1004A VAL* 4.3 1.8 - - + -
1005A ASN* 4.5 0.7 - - - +
1030A PHE* 3.7 27.1 - - + -
1031A GLY* 1.3 78.6 - - - +
1033A VAL* 1.3 65.3 + - - +
1034A ASN* 3.4 4.4 + - - +
1035A GLY* 2.9 15.1 + - - -
1036A MET* 2.7 48.6 + - - +
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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