Contacts of the helix formed by residues 1199 - 1208 (chain C) in PDB entry 4DDG
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 THR1199 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1191C GLU* 6.0 3.8 - - - -
1194C ILE* 4.2 2.2 - - - -
1197C GLY 3.6 4.5 + - - +
1198C ARG* 1.3 77.5 - - - +
1200C VAL* 1.3 67.8 + - - +
1201C LYS* 3.7 5.5 + - - +
1202C GLU* 3.2 41.6 + - - +
1203C PHE* 3.1 21.8 + - - +
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Residues in contact with VAL1200 (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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1183C LEU* 3.6 33.0 - - + +
1184C GLN* 4.2 5.4 - - + -
1187C SER* 3.4 35.0 - - - +
1190C PHE* 5.4 6.1 - - + -
1191C GLU* 5.2 12.4 - - + +
1194C ILE* 4.1 15.6 - - + +
1199C THR* 1.3 76.0 - - - +
1201C LYS* 1.3 60.6 + - + +
1203C PHE* 3.2 6.8 + - + +
1204C CYS* 2.9 30.6 + - - -
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Residues in contact with LYS1201 (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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1184C GLN* 3.4 35.2 - - + +
1199C THR* 3.4 5.5 + - - +
1200C VAL* 1.3 81.9 - - + +
1202C GLU* 1.3 61.0 + - + +
1204C CYS* 3.2 6.4 + - - +
1205C GLN* 2.9 53.5 + - + +
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Residues in contact with GLU1202 (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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1197C GLY 4.7 0.9 - - - +
1198C ARG* 3.4 15.3 - - + +
1199C THR* 3.2 43.0 + - - +
1200C VAL 3.3 0.2 - - - -
1201C LYS* 1.3 75.2 - - + +
1203C PHE* 1.3 59.6 + - - +
1205C GLN* 3.2 15.0 + - - +
1206C GLN* 2.9 51.0 + - - +
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Residues in contact with PHE1203 (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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1183C LEU* 4.2 16.8 - - + -
1194C ILE* 4.0 32.5 - - + -
1195C GLU* 4.0 11.4 - - - -
1198C ARG* 3.5 39.4 - - + +
1199C THR 3.1 14.1 + - - +
1200C VAL* 3.2 11.9 + - + +
1202C GLU* 1.3 75.0 - - - +
1204C CYS* 1.3 59.5 + - - +
1206C GLN* 4.7 1.6 - - - -
1207C GLU* 2.9 37.9 + - + -
1208C VAL* 3.5 21.1 - - + +
1216C ASP* 5.8 0.9 - - + -
1218C ILE* 3.9 20.0 - - + -
1219C HIS* 3.7 25.4 - + - -
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Residues in contact with CYS1204 (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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1180C SER* 3.2 33.4 - - - +
1183C LEU* 3.6 38.1 - - - -
1184C GLN* 3.8 15.7 - - - +
1200C VAL* 2.9 17.6 + - - +
1201C LYS 3.5 8.1 - - - +
1202C GLU 3.2 0.2 - - - -
1203C PHE* 1.3 78.8 - - - +
1205C GLN* 1.3 61.5 + - + +
1206C GLN 3.2 0.9 + - - -
1208C VAL* 3.3 9.6 + - - -
1209C GLU* 2.8 32.0 + - - +
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Residues in contact with GLN1205 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A GLN* 3.9 40.0 - - - +
1201C LYS* 2.9 50.0 + - + +
1202C GLU* 3.2 14.9 + - - +
1204C CYS* 1.3 76.1 - - - +
1206C GLN* 1.3 57.9 + - - +
1209C GLU* 4.5 16.9 - - - +
1210C PRO* 3.2 18.6 - - - +
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Residues in contact with GLN1206 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A SER 5.2 0.8 - - - +
92A GLN* 4.4 31.7 + - + +
1198C ARG* 3.0 43.7 + - - +
1202C GLU* 2.9 29.5 + - - +
1205C GLN* 1.3 80.8 - - - +
1207C GLU* 1.3 65.1 + - - +
1208C VAL 3.5 0.7 - - - -
1210C PRO* 3.1 21.1 - - - +
1213C LYS* 3.5 18.5 + - - +
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Residues in contact with GLU1207 (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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1176C ARG* 4.4 1.6 + - - -
1195C GLU* 5.3 0.5 - - - +
1198C ARG* 3.5 27.7 + - - +
1203C PHE* 2.9 40.3 + - + +
1206C GLN* 1.3 81.7 - - - +
1208C VAL* 1.3 60.2 + - - +
1213C LYS* 3.9 31.0 + - + +
1214C GLU* 3.5 22.2 - - + +
1219C HIS* 2.9 19.5 + - + +
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Residues in contact with VAL1208 (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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1093C TYR* 4.6 1.3 - - - +
1176C ARG* 3.1 53.2 + - - +
1179C THR* 4.1 10.1 - - + -
1180C SER* 3.7 19.7 - - - +
1183C LEU* 4.1 8.3 - - + -
1203C PHE* 3.5 16.6 - - + +
1204C CYS* 3.3 25.0 + - + -
1206C GLN 3.5 1.6 + - - -
1207C GLU* 1.3 79.9 - - - +
1209C GLU* 1.3 67.7 + - - +
1210C PRO* 3.3 3.1 - - - +
1219C HIS* 3.5 21.8 - - + +
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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