Contacts of the helix formed by residues 1185 - 1192 (chain A) in PDB entry 6RQT
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 VAL1185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1030A VAL* 3.0 25.1 + - + +
1032A VAL* 3.7 27.4 - - + -
1038A ILE* 4.2 11.9 - - + -
1050A TYR* 4.3 18.2 - - + -
1179A ILE* 5.9 0.2 - - + -
1183A GLU* 4.1 5.4 - - - +
1184A ALA* 1.3 75.5 - - - +
1186A GLY* 1.3 57.4 + - - +
1187A ILE 3.3 1.3 + - - -
1188A ILE* 3.3 4.0 + - - +
1189A ALA* 2.9 32.9 + - + +
1581A HIS* 5.4 4.3 - - + -
1584A LEU* 3.7 38.8 - - + -
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Residues in contact with GLY1186 (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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1024A THR 4.7 0.3 - - - +
1027A LEU* 3.1 43.8 - - - +
1028A GLU 3.6 12.3 - - - -
1030A VAL* 3.6 10.4 + - - +
1184A ALA* 3.4 4.2 - - - +
1185A VAL* 1.3 79.1 - - - +
1187A ILE* 1.3 64.4 + - - +
1190A SER* 3.3 14.7 + - - -
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Residues in contact with ILE1187 (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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596A HIS 5.6 1.1 - - - -
597A LYS* 4.8 11.2 - - + +
1024A THR* 4.4 18.2 - - + +
1028A GLU* 4.5 6.7 - - + +
1184A ALA* 4.9 4.1 + - + -
1186A GLY* 1.3 81.4 - - - +
1188A ILE* 1.3 53.9 + - + +
1190A SER* 3.0 9.2 + - - +
1191A GLN* 2.6 42.0 + - + +
1077B ASP* 3.3 37.5 - - - +
1078B ALA* 4.9 1.1 - - - -
1080B ILE* 3.7 23.6 - - + +
1081B GLY* 3.6 39.0 - - - +
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Residues in contact with ILE1188 (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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597A LYS* 3.4 36.6 - - + +
660A PRO* 3.3 40.4 - - + +
1183A GLU* 3.2 27.4 - - - +
1184A ALA 3.7 8.5 - - - +
1185A VAL* 3.3 5.7 + - - +
1187A ILE* 1.3 76.2 - - + +
1189A ALA* 1.3 65.2 + - - +
1191A GLN* 3.7 11.0 - - - +
1192A SER* 3.4 19.8 + - - -
1581A HIS* 3.3 26.1 - - + +
1081B GLY 4.2 1.6 - - - +
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Residues in contact with ALA1189 (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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1027A LEU* 3.7 22.0 - - + -
1185A VAL* 2.9 19.7 + - + +
1188A ILE* 1.3 79.6 - - - +
1190A SER* 1.3 60.7 + - - +
1191A GLN 3.4 0.3 + - - -
1192A SER* 3.8 7.3 + - - -
1193A VAL* 4.2 6.4 + - - +
1581A HIS* 4.1 12.5 - - + +
1582A LEU* 5.6 0.5 - - - +
1584A LEU* 4.1 15.7 - - + -
1585A ILE* 3.3 33.8 - - + +
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Residues in contact with SER1190 (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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1019A LEU* 4.9 0.2 - - - +
1020A GLN* 2.9 26.2 + - - +
1023A LEU* 3.2 48.1 + - - -
1024A THR* 3.8 9.3 + - - +
1027A LEU* 5.6 2.5 - - - -
1186A GLY 3.3 10.1 + - - -
1187A ILE* 3.0 11.2 + - - +
1189A ALA* 1.3 76.9 - - - +
1191A GLN* 1.3 62.4 + - - +
1193A VAL* 4.0 11.1 - - - +
1194A GLY 3.7 4.2 + - - -
1585A ILE* 5.1 2.7 - - - -
1077B ASP* 5.6 0.3 + - - -
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Residues in contact with GLN1191 (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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595A LEU 4.4 0.9 - - - +
596A HIS* 3.7 32.8 - - + +
597A LYS* 4.0 12.3 - - + +
659A THR* 5.2 1.4 + - - -
660A PRO* 3.1 9.1 - - - +
661A THR* 2.6 29.8 + - - +
1020A GLN* 4.6 6.5 - - - +
1187A ILE* 2.6 26.1 + - + +
1188A ILE* 3.7 12.6 - - - +
1189A ALA 3.2 0.4 - - - -
1190A SER* 1.3 74.6 - - - +
1192A SER* 1.3 76.4 + - - +
1193A VAL 3.1 1.1 - - - -
1194A GLY* 2.7 22.9 + - - -
1195A GLU* 2.8 39.1 + - - +
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Residues in contact with SER1192 (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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660A PRO 3.3 3.3 + - - -
661A THR* 3.3 34.3 + - - -
1188A ILE* 3.4 13.5 + - - +
1189A ALA 3.8 4.2 + - - -
1190A SER 3.6 0.4 - - - -
1191A GLN* 1.3 96.2 + - - +
1193A VAL* 1.3 56.9 + - - +
1194A GLY 3.5 0.2 - - - -
1196A PRO* 3.8 12.0 - - - +
1570A PHE* 3.9 5.7 - - - -
1577A VAL* 3.8 22.5 - - - +
1578A SER* 6.0 0.2 - - - -
1581A HIS* 4.6 13.4 + - - -
1582A LEU* 6.0 3.6 - - - -
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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