Contacts of the helix formed by residues 1025 - 1032 (chain A) in PDB entry 1SIW
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 GLY1025 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567A VAL* 5.0 3.6 - - - -
568A GLY* 3.4 13.4 - - - -
1013A SER* 2.7 15.8 + - - -
1023A ASN 3.5 0.2 + - - -
1024A ALA* 1.3 72.2 - - - +
1026A TYR* 1.3 63.6 + - - +
1027A THR 3.3 2.5 - - - -
1028A ASN* 3.3 23.1 + - - +
1029A VAL* 3.2 19.4 + - - +
1035A TRP* 4.5 10.9 - - - -
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Residues in contact with TYR1026 (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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568A GLY 3.4 21.5 - - - +
569A GLN* 5.1 0.2 - - - -
570A SER* 4.4 13.7 - - - -
1013A SER 3.1 6.0 + - - +
1014A GLY* 4.4 3.4 - - - -
1015A LEU* 3.6 37.7 - - + +
1020A VAL* 4.0 34.1 - - + +
1021A SER 5.4 1.1 - - - -
1023A ASN* 3.1 25.1 + - + +
1024A ALA 3.2 1.0 + - - -
1025A GLY* 1.3 77.6 - - - +
1027A THR* 1.3 57.8 + - - +
1030A HIS* 2.9 71.6 + + + +
1031A GLU* 6.5 0.2 - - + -
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Residues in contact with THR1027 (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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971A TRP* 4.4 15.7 - - + -
1012A TRP 4.2 1.9 + - - +
1013A SER* 2.8 45.2 + - - +
1015A LEU* 3.7 31.9 - - + -
1026A TYR* 1.3 72.1 - - - +
1028A ASN* 1.3 64.6 + - - +
1031A GLU* 2.7 47.1 + - + +
1032A LEU 3.4 1.0 + - - -
1033A ILE* 3.6 21.6 + - - +
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Residues in contact with ASN1028 (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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333A TYR* 4.1 0.9 - - - -
402A LEU* 4.0 9.1 - - - +
1013A SER* 3.5 13.6 - - - -
1025A GLY* 3.3 20.6 + - - +
1027A THR* 1.3 79.6 + - - +
1029A VAL* 1.3 62.1 + - - +
1032A LEU* 3.2 22.2 + - - -
1033A ILE* 2.8 35.8 + - - +
1034A PRO 3.4 20.4 + - - -
1035A TRP* 3.6 42.7 + - + +
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Residues in contact with VAL1029 (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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329A TYR* 4.4 5.2 - - + +
333A TYR* 2.8 51.4 + - + +
567A VAL 3.6 22.7 - - - +
568A GLY* 4.0 4.5 - - - +
569A GLN* 4.6 8.3 - - - +
1025A GLY 3.2 12.9 + - - +
1028A ASN* 1.3 78.6 - - - +
1030A HIS* 1.3 82.8 + - + +
1032A LEU* 3.8 6.8 - - - +
1035A TRP* 4.0 19.5 - - + -
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Residues in contact with HIS1030 (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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568A GLY 2.9 25.6 + - - -
569A GLN* 3.1 19.5 + - - -
980A ARG* 5.2 2.9 + - - -
1026A TYR* 2.9 66.8 + + + +
1029A VAL* 1.3 89.0 - - + +
1031A GLU* 1.3 70.5 + - + +
1032A LEU* 3.4 6.4 - - - +
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Residues in contact with GLU1031 (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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980A ARG* 3.0 25.1 + - - +
981A ASP 3.9 0.7 - - - +
982A HIS* 3.1 25.5 + - - +
984A HIS* 3.0 39.1 + - - -
985A LEU* 4.1 25.8 - - + +
1015A LEU* 5.8 2.6 - - + +
1027A THR* 2.7 27.5 + - + +
1030A HIS* 1.3 83.0 - - + +
1032A LEU* 1.3 67.2 + - - +
1033A ILE* 3.2 14.5 + - + -
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Residues in contact with LEU1032 (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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332A ARG* 4.9 7.0 - - - +
333A TYR* 4.3 10.5 - - + +
401A ASN* 3.3 9.7 - - - +
402A LEU* 2.7 49.3 + - + +
403A GLU* 3.6 24.0 - - + -
980A ARG* 3.5 32.5 - - - +
1028A ASN 3.2 11.2 + - - +
1029A VAL 3.8 18.8 - - - +
1030A HIS 4.5 4.9 - - - +
1031A GLU* 1.3 81.2 - - - +
1033A ILE* 1.3 60.5 + - - +
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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