Contacts of the helix formed by residues 1097 - 1109 (chain C) in PDB entry 6TYF
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 VAL1097 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1095C ASP* 3.4 9.0 - - - +
1096C THR* 1.3 85.4 - - + +
1098C GLY* 1.3 68.9 + - - +
1099C ARG 3.4 0.7 - - - -
1100C VAL* 3.5 4.6 + - - +
1101C LYS* 3.1 39.6 + - + +
1116C GLY* 5.5 4.9 - - - -
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Residues in contact with GLY1098 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091C ILE* 3.7 12.6 - - - +
1095C ASP* 2.6 35.4 + - - -
1097C VAL* 1.3 73.7 - - - +
1099C ARG* 1.3 63.9 + - - +
1101C LYS* 3.4 6.2 + - - +
1102C VAL* 3.1 27.5 + - - +
1113C PRO* 4.5 1.8 - - - +
1114C GLU 5.2 4.5 - - - -
1116C GLY 5.0 1.1 - - - -
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Residues in contact with ARG1099 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049C TYR* 3.5 53.0 + - - +
1054C GLN* 2.9 47.5 + - - +
1091C ILE 3.1 26.1 + - - +
1093C SER 3.0 22.2 + - - +
1094C ASP* 4.0 5.3 - - - +
1095C ASP* 3.0 21.6 + - - +
1096C THR* 3.9 13.9 - - - +
1098C GLY* 1.3 77.6 - - - +
1100C VAL* 1.3 66.3 + - + +
1102C VAL* 3.4 7.1 + - - +
1103C TYR* 3.1 20.6 + - - +
423D ASP* 4.4 2.7 + - - +
424D TYR* 5.3 1.6 + - + -
106F GLU* 3.9 21.4 + - - -
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Residues in contact with VAL1100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096C THR 3.8 11.4 - - - +
1097C VAL* 3.5 8.6 + - - +
1098C GLY 3.3 0.4 - - - -
1099C ARG* 1.3 78.4 - - + +
1101C LYS* 1.3 64.3 + - + +
1103C TYR* 3.0 8.5 + - + +
1104C GLU* 2.8 50.1 + - + +
106F GLU* 3.5 42.6 - - + +
110F ALA* 4.5 6.1 - - + -
113F ARG* 4.0 15.5 - - - +
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Residues in contact with LYS1101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097C VAL* 3.1 27.3 + - - +
1098C GLY* 4.0 3.1 - - - +
1100C VAL* 1.3 79.7 - - + +
1102C VAL* 1.3 57.0 + - - +
1104C GLU* 3.9 15.9 - - - +
1105C ALA* 2.9 30.1 + - - +
1113C PRO* 3.5 26.9 - - + +
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Residues in contact with VAL1102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091C ILE* 3.7 34.5 - - + +
1098C GLY 3.1 16.9 + - - +
1099C ARG* 3.5 10.8 - - - +
1100C VAL 3.1 0.2 - - - -
1101C LYS* 1.3 77.0 - - - +
1103C TYR* 1.3 65.4 + - - +
1105C ALA* 3.8 1.1 - - - +
1106C ILE* 3.0 47.4 + - + +
1112C ILE* 3.9 13.0 - - + -
1113C PRO* 3.9 19.7 - - + -
424D TYR* 4.0 12.6 - - + +
547D LEU* 4.2 13.2 - - + -
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Residues in contact with TYR1103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045C SER* 5.5 1.9 + - - -
1046C THR* 3.7 20.3 + - + -
1099C ARG 3.1 13.0 + - - +
1100C VAL* 3.0 12.2 + - + +
1102C VAL* 1.3 80.1 - - - +
1104C GLU* 1.3 60.8 + - + +
1106C ILE* 3.5 5.0 + - - +
1107C VAL* 3.4 25.8 + - + +
424D TYR* 3.8 16.6 - - - -
453D LYS* 5.1 8.7 - - - +
454D PRO* 4.4 15.2 - - + +
457D MET* 3.5 28.3 - - + +
473D LYS* 4.6 1.6 - - - +
107F VAL* 2.6 66.1 - - + +
110F ALA* 5.0 7.0 - - + -
111F LEU* 4.7 7.2 - - + -
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Residues in contact with GLU1104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100C VAL* 2.8 26.7 + - - +
1101C LYS* 4.0 16.3 - - - +
1103C TYR* 1.3 76.9 - - - +
1105C ALA* 1.3 61.2 + - - +
1106C ILE 3.2 0.2 + - - -
1107C VAL* 3.2 12.8 - - - +
1108C LYS* 3.0 35.0 + - + +
110F ALA* 4.0 16.3 - - + +
113F ARG* 2.1 43.2 + - - -
114F LEU* 4.3 25.2 - - + +
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Residues in contact with ALA1105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101C LYS 2.9 21.8 + - - +
1102C VAL* 3.3 4.5 + - - +
1104C GLU* 1.3 76.3 - - - +
1106C ILE* 1.3 60.6 + - - +
1108C LYS* 3.9 1.8 - - - -
1109C GLY 3.2 1.4 + - - -
1110C GLU* 3.1 46.1 + - + +
1111C ASN 3.3 28.3 - - - +
1112C ILE* 4.5 3.4 - - + -
1113C PRO* 3.9 9.2 - - + -
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Residues in contact with ILE1106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102C VAL* 3.0 28.1 + - + +
1103C TYR* 3.9 4.7 - - - +
1104C GLU 3.1 0.2 - - - -
1105C ALA* 1.3 77.2 - - - +
1107C VAL* 1.3 64.6 + - - +
1109C GLY* 3.2 12.6 + - - -
1110C GLU 5.2 0.4 - - - -
1112C ILE* 4.3 11.9 - - + -
424D TYR* 3.9 22.2 - - + +
454D PRO* 3.7 27.4 - - + +
455D PHE* 3.7 55.2 - - + +
458D LYS* 3.9 9.5 - - - +
547D LEU* 4.9 3.4 - - + -
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Residues in contact with VAL1107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103C TYR* 3.4 15.5 + - + +
1104C GLU* 3.2 11.2 - - - +
1106C ILE* 1.3 75.8 - - - +
1108C LYS* 1.3 60.4 + - + +
454D PRO* 4.3 11.2 - - + +
457D MET* 4.1 21.5 - - + -
458D LYS* 3.0 29.9 - - - +
461D VAL* 5.7 1.0 - - - +
469D ILE* 4.2 19.8 - - + +
111F LEU* 4.1 21.5 - - + -
114F LEU* 3.6 25.4 - - + -
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Residues in contact with LYS1108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104C GLU* 3.0 27.7 + - + +
1105C ALA 4.2 0.4 - - - +
1106C ILE 3.2 0.2 - - - -
1107C VAL* 1.3 78.3 - - - +
1109C GLY* 1.3 59.2 + - - +
1110C GLU* 3.2 42.6 + - + +
458D LYS* 4.0 8.1 - - - +
69E ASN* 3.8 10.4 - - - +
114F LEU* 3.4 39.1 - - + +
118F ASP* 6.1 1.6 - - - -
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Residues in contact with GLY1109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105C ALA 3.2 2.8 + - - -
1106C ILE 3.2 13.5 + - - -
1107C VAL 3.3 0.6 - - - -
1108C LYS* 1.3 76.0 - - - +
1110C GLU* 1.3 59.9 + - - +
458D LYS* 4.0 11.8 - - - +
65E ASN* 2.9 18.2 + - - +
69E ASN* 2.6 26.2 + - - -
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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