Contacts of the helix formed by residues 1096 - 1105 (chain A) in PDB entry 1F5T
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 LYS1096 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1092A LEU* 4.0 12.1 - - + +
1093A ASP* 2.9 31.1 + - + +
1095A ASN* 1.3 81.9 - - + +
1097A VAL* 1.3 61.7 + - - +
1098A HIS 3.6 1.3 - - - -
1099A ASP* 4.1 12.3 + - + +
1100A GLU* 3.5 22.7 + - - +
2111B GLU* 3.3 39.9 + - + +
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Residues in contact with VAL1097 (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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1083A GLU* 3.4 39.3 - - + +
1086A LEU* 3.8 10.8 - - + +
1087A THR* 3.7 12.8 - - - +
1092A LEU* 3.6 28.0 - - + +
1093A ASP 3.2 18.6 - - - +
1094A ILE* 3.3 20.2 + - + +
1095A ASN 3.5 0.4 - - - -
1096A LYS* 1.3 77.2 - - - +
1098A HIS* 1.3 67.7 + - - +
1100A GLU* 4.6 0.4 - - - -
1101A ALA* 3.0 21.1 + - - +
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Residues in contact with HIS1098 (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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252A NI 2.0 35.6 - - + +
1013A ARG* 3.6 20.7 + - - -
1017A GLU* 5.0 4.3 + - - -
1079A HIS* 2.6 18.8 + + - -
1083A GLU* 2.0 24.1 + - - +
1094A ILE 4.7 1.0 + - - -
1095A ASN 5.3 0.8 + - - -
1096A LYS 3.6 0.2 - - - -
1097A VAL* 1.3 76.8 - - - +
1099A ASP* 1.3 59.6 + - - +
1101A ALA* 3.0 4.0 + - - +
1102A ASP* 2.7 40.5 + - + +
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Residues in contact with ASP1099 (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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1095A ASN 3.9 17.7 - - - +
1096A LYS* 4.1 9.9 - - + +
1098A HIS* 1.3 81.3 + - - +
1100A GLU* 1.3 64.2 + - - +
1102A ASP* 3.2 20.0 + - - +
1103A ARG* 3.6 18.2 + - - +
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Residues in contact with GLU1100 (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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1086A LEU* 3.7 20.2 - - + -
1092A LEU* 4.3 4.2 - - + +
1096A LYS 3.5 16.5 + - - +
1097A VAL 3.9 0.2 - - - +
1098A HIS 3.2 0.4 - - - -
1099A ASP* 1.3 78.1 - - - +
1101A ALA* 1.3 59.1 + - - +
1103A ARG* 2.9 44.6 + - - +
1104A TRP* 3.1 39.1 + - + +
2108B MET* 3.7 1.6 - - - -
2109B SER* 3.0 45.2 + - - -
2112B VAL* 3.5 19.9 - - + +
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Residues in contact with ALA1101 (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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1079A HIS* 3.7 11.2 + - - +
1082A ALA* 4.0 3.2 - - + +
1083A GLU* 3.5 39.0 - - + +
1086A LEU* 3.8 8.0 - - + +
1097A VAL 3.0 15.7 + - - +
1098A HIS 3.0 4.1 + - - +
1100A GLU* 1.3 74.7 - - - +
1102A ASP* 1.3 56.1 + - - +
1103A ARG 3.0 5.6 - - - -
1104A TRP* 3.7 7.6 - - - +
1105A GLU* 3.1 30.3 + - - +
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Residues in contact with ASP1102 (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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251A NI 1.7 87.8 - - - +
1010A MET* 2.6 15.1 - - - +
1013A ARG* 3.8 15.5 + - - +
1079A HIS* 4.4 0.4 - - - -
1098A HIS* 2.7 19.8 + - + +
1099A ASP* 3.4 14.8 - - - +
1100A GLU 3.1 0.6 - - - -
1101A ALA* 1.3 73.2 - - - +
1103A ARG* 1.3 55.2 + - + +
1105A GLU* 3.0 10.8 - - - -
1106A HIS* 2.8 1.2 + - - -
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Residues in contact with ARG1103 (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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1003A ASP 5.8 2.7 - - - +
1005A VAL* 4.1 17.6 - - + +
1099A ASP* 3.8 18.6 + - - +
1100A GLU* 2.9 40.2 + - - +
1102A ASP* 1.3 81.1 - - + +
1104A TRP* 1.3 66.0 + - + +
1105A GLU 3.2 2.4 + - - -
1106A HIS* 3.4 15.1 + - - +
1107A VAL* 4.0 7.1 + - - +
2107B VAL* 3.0 58.0 + - + +
2108B MET 4.2 0.2 - - - -
2109B SER* 3.5 15.6 - - - +
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Residues in contact with TRP1104 (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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1082A ALA* 4.2 20.2 - - + -
1085A LEU* 4.3 15.5 - - + -
1086A LEU* 3.6 31.6 - - + -
1090A ILE* 4.2 10.5 - - + -
1100A GLU* 3.1 38.5 + - + +
1101A ALA* 3.5 4.5 + - - +
1103A ARG* 1.3 72.3 - - - +
1105A GLU* 1.3 66.5 + - - +
1106A HIS 3.1 2.5 - - - -
1107A VAL* 3.0 21.1 + - + +
1108A MET* 3.2 19.6 + - + +
2085B LEU* 4.5 5.8 - - + -
2104B TRP* 3.4 45.3 - + + -
2107B VAL* 3.1 34.6 + - + +
2108B MET* 4.4 14.1 - - + -
2112B VAL* 4.3 13.9 - - + -
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Residues in contact with GLU1105 (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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251A NI 1.5 42.7 - - - +
1009A GLU* 3.9 5.5 - - - +
1010A MET* 2.4 4.0 - - - +
1013A ARG* 2.3 31.3 + - - -
1075A VAL* 4.1 14.1 - - + +
1078A LYS* 3.6 34.9 - - - +
1079A HIS* 3.6 23.7 + - - +
1082A ALA* 4.9 0.6 - - - +
1101A ALA 3.1 9.6 + - - +
1102A ASP* 2.1 15.7 - - - +
1104A TRP* 1.3 78.3 - - - +
1106A HIS* 1.3 80.9 + - + +
1107A VAL 3.7 0.5 + - - -
1108A MET 4.8 0.2 - - - +
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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