Contacts of the helix formed by residues 1099 - 1108 (chain A) in PDB entry 6A5T
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 GLY1099 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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831A LYS* 5.8 2.7 - - - -
1081A MET* 3.5 27.3 - - - +
1098A LEU* 1.3 76.8 - - - +
1100A VAL* 1.3 66.9 + - - -
1101A PRO* 4.1 0.2 - - - -
1102A ARG* 3.2 4.0 + - - +
1103A LEU* 3.0 21.7 + - - +
1358A VAL* 3.8 11.3 - - - +
1361A PHE* 5.9 0.8 - - - -
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Residues in contact with VAL1100 (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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831A LYS* 4.7 28.1 - - + +
834A GLU* 3.7 33.4 - - + -
835A THR* 4.2 14.6 - - + -
838A ILE* 4.6 9.0 - - + -
1078A ALA* 4.0 14.1 - - + +
1081A MET* 3.6 21.2 - - + +
1099A GLY* 1.3 71.8 - - - -
1101A PRO* 1.3 70.4 - - + +
1103A LEU* 3.3 3.9 + - + +
1104A LYS* 2.9 23.5 + - + +
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Residues in contact with PRO1101 (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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831A LYS* 5.1 11.9 - - - +
1097A THR* 3.9 16.2 - - + -
1098A LEU 3.2 17.0 - - - +
1100A VAL* 1.3 94.1 - - + +
1102A ARG* 1.3 56.4 + - - +
1104A LYS* 3.3 12.4 + - + +
1105A GLU* 2.9 35.9 + - - +
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Residues in contact with ARG1102 (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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1097A THR* 3.7 41.7 + - + +
1098A LEU* 4.1 2.7 - - - -
1099A GLY 3.2 7.8 + - - +
1101A PRO* 1.3 80.1 - - - +
1103A LEU* 1.3 64.4 + - - +
1105A GLU* 3.0 10.0 + - - +
1106A ILE* 2.9 42.6 + - + +
1113A ILE* 3.4 37.4 - - - +
1114A LYS 5.4 1.0 - - - +
1115A THR 4.9 4.4 + - - -
1333A ASN* 3.7 31.6 + - - +
1334A SER* 5.4 0.2 - - - +
1335A PHE* 6.1 0.4 - - - -
1354A GLU* 3.3 26.6 + - - +
1358A VAL* 3.6 26.2 - - + +
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Residues in contact with LEU1103 (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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838A ILE* 4.8 15.5 - - + -
842A LEU* 5.7 1.1 - - + -
1074A ILE* 5.2 13.7 - - + -
1075A GLY* 5.8 0.2 - - - -
1078A ALA* 3.7 29.6 - - + -
1081A MET* 4.2 9.2 - - + -
1099A GLY 3.0 15.0 + - - +
1100A VAL* 3.9 4.7 - - + +
1102A ARG* 1.3 77.6 - - - +
1104A LYS* 1.3 56.8 + - - +
1106A ILE* 3.9 6.9 - - + +
1107A LEU* 3.0 49.7 + - + +
1355A ILE* 4.9 19.1 - - + -
1358A VAL* 5.0 14.3 - - + +
1359A ILE* 5.2 13.5 - - + -
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Residues in contact with LYS1104 (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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834A GLU* 3.7 36.8 + - + +
838A ILE* 4.7 9.4 - - + +
841A ARG* 5.3 1.1 - - - +
1100A VAL* 2.9 19.4 + - + +
1101A PRO* 3.3 10.8 - - + +
1103A LEU* 1.3 73.6 - - - +
1105A GLU* 1.3 62.1 + - + +
1106A ILE 3.0 4.5 - - - -
1107A LEU* 4.1 1.7 - - - -
1108A ASN* 3.1 53.0 + - - +
-32N T 4.2 16.5 + - - -
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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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1097A THR* 5.2 5.1 + - - +
1101A PRO* 2.9 21.8 + - - +
1102A ARG* 3.6 12.6 + - - +
1104A LYS* 1.3 79.1 - - + +
1106A ILE* 1.3 61.6 + - + +
1108A ASN* 4.4 6.1 - - - +
1109A VAL* 4.4 0.3 - - - -
1110A ALA* 3.8 28.4 + - + +
1112A ASN 4.6 3.5 - - - +
1113A ILE* 3.2 30.0 - - + +
1114A LYS* 3.2 40.1 + - - +
1335A PHE* 5.7 1.2 - - - -
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Residues in contact with ILE1106 (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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1102A ARG* 2.9 49.1 + - + +
1103A LEU* 4.1 8.1 - - + +
1105A GLU* 1.3 84.0 - - + +
1107A LEU* 1.3 71.6 + - + +
1108A ASN 3.3 0.2 - - - -
1109A VAL* 3.3 21.5 - - - +
1113A ILE* 6.0 1.1 - - + -
1335A PHE* 4.5 14.6 - - + -
1351A LEU* 4.0 25.6 - - + -
1354A GLU* 3.8 31.9 - - + +
1355A ILE* 4.4 17.9 - - + +
1358A VAL* 5.2 1.3 - - + -
1378A MET* 4.3 1.7 - - + +
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Residues in contact with LEU1107 (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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838A ILE* 4.2 9.6 - - + -
841A ARG* 4.5 13.2 - - - +
842A LEU* 3.6 39.7 - - + -
1074A ILE* 6.0 1.3 - - + -
1103A LEU* 3.0 36.3 + - + +
1104A LYS* 4.4 1.6 - - - +
1106A ILE* 1.3 86.6 - - + +
1108A ASN* 1.3 60.2 + - - +
1109A VAL* 3.0 8.7 + - - +
1355A ILE* 5.2 2.5 - - + -
1374A LEU* 4.2 23.6 - - + -
1378A MET* 4.2 14.9 - - - +
1386A ALA* 4.0 0.3 - - - +
1387A ILE* 3.1 36.9 + - + +
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Residues in contact with ASN1108 (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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834A GLU* 5.2 0.4 + - - -
841A ARG* 2.3 47.1 + - - +
1104A LYS* 3.1 38.5 + - - +
1105A GLU* 4.0 3.1 - - - +
1106A ILE 4.1 1.3 - - - -
1107A LEU* 1.3 73.1 - - - +
1109A VAL* 1.3 66.1 + - - +
1110A ALA* 2.7 11.9 + - + +
1386A ALA* 4.5 0.9 - - - -
1388A THR* 3.5 13.6 - - + +
-30N A 5.1 2.9 - - - +
-29N T 3.1 18.8 + - - +
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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