Contacts of the helix formed by residues 1109 - 1122 (chain C) in PDB entry 6VVT
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 PRO1109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1080C LEU* 3.6 17.9 - - + +
1081C THR* 4.3 6.2 - - + -
1085C ASP* 3.6 22.9 - - + +
1086C ASP* 4.5 1.6 - - - +
1107C GLY 3.8 5.8 - - - +
1108C ILE* 1.3 89.6 - - + +
1110C GLU* 1.3 65.4 + - - +
1111C SER* 3.1 1.6 - - - +
1112C PHE* 3.0 15.8 + - + -
1113C LYS 3.4 6.9 + - - -
420D LYS* 3.7 7.6 - - - +
1253D VAL 5.3 0.9 - - - +
1254D ILE 3.7 18.8 - - - +
1255D ILE 3.1 27.4 - - - +
1256D GLY* 4.1 7.2 - - - +
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Residues in contact with GLU1110 (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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1044C THR* 5.9 0.4 - - - -
1045C GLN* 4.2 18.8 - - + +
1085C ASP* 2.9 30.9 + - - +
1087C THR* 3.4 22.6 + - + +
1108C ILE 3.4 3.3 + - - +
1109C PRO* 1.3 71.9 - - - +
1111C SER* 1.3 63.5 + - - +
1113C LYS* 3.1 36.6 + - - +
1114C VAL* 2.9 30.2 + - + +
86D LYS* 6.0 0.3 - - - +
89D ARG* 3.1 48.0 + - - +
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Residues in contact with SER1111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044C THR* 5.4 3.6 - - - -
1046C GLN* 4.7 6.5 - - - -
1085C ASP* 3.1 19.2 - - - -
1109C PRO* 4.0 4.0 - - - +
1110C GLU* 1.3 79.0 - - - +
1112C PHE* 1.3 69.6 + - - +
1114C VAL* 3.3 9.4 + - - +
1115C LEU* 2.9 20.8 + - - +
1118C GLU* 5.2 0.2 - - - +
416D ASN 5.1 0.2 - - - -
417D LEU* 3.1 30.1 - - - +
420D LYS* 2.8 24.9 + - - -
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Residues in contact with PHE1112 (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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1108C ILE* 4.3 14.4 - - + -
1109C PRO* 3.0 14.4 + - + +
1111C SER* 1.3 83.0 + - - +
1113C LYS* 1.3 64.5 + - - +
1115C LEU* 2.9 27.8 + - + +
1116C LEU* 3.1 45.3 + - + +
1128C VAL* 5.5 3.4 - - + -
1138C MET* 4.9 6.5 - - - -
7D PHE* 5.0 12.6 - + - -
10D LEU* 4.3 23.1 - - + -
417D LEU* 4.4 3.1 - - - -
1222D LEU* 4.6 2.5 - - + -
1254D ILE* 3.6 32.3 - - + +
1255D ILE* 3.3 39.3 - - + -
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Residues in contact with LYS1113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087C THR* 5.6 2.2 + - - -
1108C ILE* 3.3 32.5 - - + +
1109C PRO 3.7 5.2 - - - +
1110C GLU* 3.1 40.6 + - - +
1112C PHE* 1.3 78.0 - - - +
1114C VAL* 1.3 63.3 + - - +
1115C LEU 3.3 0.2 + - - -
1116C LEU* 3.3 11.3 + - - +
1117C LYS* 3.3 22.0 + - - +
1138C MET* 3.6 37.0 - - + +
1139C ARG 4.8 3.0 - - - +
86D LYS* 5.3 6.5 - - - +
89D ARG* 5.8 0.2 - - - +
90D GLU* 4.0 24.2 + - - +
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Residues in contact with VAL1114 (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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1043C ILE* 4.8 7.0 - - + +
1044C THR* 5.8 3.4 - - - -
1110C GLU* 2.9 22.1 + - + +
1111C SER* 3.5 10.8 - - - +
1113C LYS* 1.3 75.2 - - - +
1115C LEU* 1.3 63.2 + - - +
1117C LYS* 3.2 7.9 + - - +
1118C GLU* 2.9 41.7 + - + +
89D ARG* 3.8 17.7 - - + +
324D LEU* 3.8 32.1 - - + -
412D ARG* 5.9 2.5 - - + -
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Residues in contact with LEU1115 (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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1111C SER 2.9 13.0 + - - +
1112C PHE* 2.9 25.0 + - + +
1114C VAL* 1.3 75.9 - - - +
1116C LEU* 1.3 63.7 + - + +
1118C GLU* 3.1 13.2 + - - +
1119C LEU* 3.0 37.6 + - + +
406D LEU* 3.4 31.6 - - + -
412D ARG 4.5 13.9 - - - +
413D PHE* 5.4 2.5 - - - -
417D LEU* 3.9 24.5 - - + -
1222D LEU* 5.3 8.5 - - + -
1254D ILE* 4.2 13.9 - - + -
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Residues in contact with LEU1116 (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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1112C PHE* 3.1 55.6 + - + +
1113C LYS* 3.7 6.3 - - - +
1115C LEU* 1.3 79.1 - - + +
1117C LYS* 1.3 63.1 + - + +
1119C LEU* 3.2 16.4 + - + +
1120C GLN* 2.9 40.2 + - - +
1126C VAL* 3.6 24.4 - - + +
1128C VAL* 5.3 8.1 - - + +
1138C MET* 4.0 26.0 - - + -
10D LEU* 5.2 7.0 - - + -
1221D TRP* 6.3 0.2 - - + -
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Residues in contact with LYS1117 (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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1113C LYS 3.3 11.1 + - - +
1114C VAL* 3.2 9.3 + - - +
1116C LEU* 1.3 79.9 - - + +
1118C GLU* 1.3 62.9 + - - +
1120C GLN* 3.2 33.9 + - - +
1121C SER* 2.9 28.7 + - - -
1137C GLU* 3.9 18.8 + - - +
89D ARG 4.5 4.5 - - - +
90D GLU* 3.1 31.7 + - - +
92D MET* 4.0 21.3 - - - +
320D ILE* 4.8 0.7 - - - -
321D PRO* 3.9 13.5 - - + -
324D LEU* 3.6 28.0 - - + -
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Residues in contact with GLU1118 (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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1114C VAL* 2.9 40.3 + - + +
1115C LEU* 3.2 24.4 - - - +
1117C LYS* 1.3 74.5 - - - +
1119C LEU* 1.3 63.4 + - - +
1121C SER* 3.5 8.6 + - - -
1122C LEU* 3.2 27.2 + - - +
320D ILE* 4.6 10.0 - - + +
324D LEU* 5.6 0.4 - - + -
402D LEU* 5.0 4.6 - - + +
405D LEU* 3.3 49.7 - - + +
406D LEU* 4.0 20.8 - - + +
412D ARG* 3.7 13.2 - - - +
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Residues in contact with LEU1119 (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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1115C LEU* 3.0 29.9 + - + +
1116C LEU* 3.2 22.9 + - + +
1118C GLU* 1.3 76.4 - - - +
1120C GLN* 1.3 62.4 + - - +
1122C LEU* 2.9 17.8 + - - +
1124C LEU* 3.0 26.0 + - + +
1126C VAL* 3.6 29.4 - - + -
12D ILE* 5.5 0.4 - - + -
406D LEU* 3.6 32.1 - - + -
1221D TRP* 4.6 19.1 - - + -
1234D LEU* 3.9 18.6 - - + -
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Residues in contact with GLN1120 (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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1116C LEU* 2.9 26.8 + - - +
1117C LYS* 3.2 38.3 + - - +
1119C LEU* 1.3 75.0 - - - +
1121C SER* 1.3 54.6 + - - +
1123C CYS* 2.6 27.4 + - - -
1124C LEU 3.5 15.7 - - - +
1126C VAL* 5.0 13.6 + - + +
1137C GLU* 6.3 0.4 - - - +
23D TRP* 3.5 31.8 - - + -
92D MET* 3.0 28.4 - - - +
318D PRO* 3.4 10.2 - - - +
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Residues in contact with SER1121 (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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1117C LYS 2.9 12.7 + - - -
1118C GLU* 3.6 5.4 - - - -
1120C GLN* 1.3 75.2 - - - +
1122C LEU* 1.3 57.8 + - - +
1123C CYS 3.2 3.3 + - - -
92D MET* 4.7 4.2 - - - -
318D PRO* 3.7 21.3 - - - +
320D ILE* 3.0 45.9 - - - +
344D TYR* 4.4 3.1 - - - -
382D PHE* 3.6 12.6 - - - -
402D LEU* 3.5 29.7 - - - +
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Residues in contact with LEU1122 (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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1118C GLU* 3.2 17.7 + - + +
1119C LEU* 2.9 12.5 + - - +
1121C SER* 1.3 72.7 - - - +
1123C CYS* 1.3 60.9 + - - +
1124C LEU* 3.2 8.6 + - + +
103D HIS* 2.8 29.1 + - - +
105D TRP* 3.7 38.6 - - + -
382D PHE* 3.8 30.3 - - + +
402D LEU* 3.4 50.0 - - + +
403D SER* 4.4 0.4 - - - -
406D LEU* 4.2 13.5 - - + -
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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