Contacts of the helix formed by residues 1183 - 1190 (chain D) in PDB entry 5UHG
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 ARG1183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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895D ARG* 6.1 1.0 - - - +
1127D PRO* 6.0 4.0 - - - +
1162D LEU 3.9 20.3 + - - -
1163D ARG* 3.0 24.6 + - - +
1165D VAL* 3.9 27.4 - - + +
1181D ILE 3.5 0.6 + - - -
1182D ASP* 1.3 72.1 + - - +
1184D ALA* 1.3 57.6 + - - +
1186D PHE* 4.0 8.3 - - + -
1187D GLU* 2.8 60.0 + - - +
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Residues in contact with ALA1184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971D SER 5.7 2.7 - - - +
1163D ARG* 4.8 10.3 - - - +
1182D ASP* 3.1 19.0 + - - +
1183D ARG* 1.3 78.8 - - - +
1185D GLU* 1.3 58.0 + - + +
1187D GLU* 3.9 3.7 - - - +
1188D ALA* 3.1 30.0 + - - +
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Residues in contact with GLU1185 (chain D).
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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1175D PHE* 3.9 7.7 - - + -
1181D ILE* 3.5 20.6 - - + +
1182D ASP* 3.1 28.4 + - + +
1184D ALA* 1.3 76.8 - - + +
1186D PHE* 1.3 60.1 + - - +
1188D ALA* 3.9 3.5 - - - +
1189D GLU* 3.0 33.4 + - - +
1218D ASP* 6.0 2.4 - - - +
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Residues in contact with PHE1186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1165D VAL* 4.0 20.2 - - + -
1167D ILE* 3.9 22.4 - - + -
1175D PHE* 4.0 14.5 - + + -
1181D ILE* 4.5 4.0 - - + +
1182D ASP 2.7 20.7 + - - +
1183D ARG* 3.7 7.2 - - + +
1184D ALA 3.3 0.2 - - - -
1185D GLU* 1.3 76.0 - - - +
1187D GLU* 1.3 74.2 + - + +
1189D GLU* 4.4 0.5 - - - +
1190D ASN* 3.2 40.0 + - - +
1201D ALA* 3.1 43.3 - - + -
1203D GLY* 3.6 26.9 - - - -
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Residues in contact with GLU1187 (chain D).
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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1183D ARG* 2.8 46.6 + - - +
1184D ALA* 3.9 2.8 - - - +
1186D PHE* 1.3 94.4 - - + +
1188D ALA* 1.3 58.4 + - - +
1190D ASN* 4.3 5.0 - - - -
1191D ARG* 2.8 53.4 + - - +
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Residues in contact with ALA1188 (chain D).
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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1184D ALA 3.1 19.5 + - - +
1185D GLU* 4.2 3.8 - - - +
1186D PHE 3.3 0.2 - - - -
1187D GLU* 1.3 77.5 - - - +
1189D GLU* 1.3 61.0 + - - +
1190D ASN 3.4 0.2 - - - -
1191D ARG* 3.6 14.1 + - - +
1192D ARG* 3.3 21.5 + - - +
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Residues in contact with GLU1189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173D THR* 3.8 16.9 - - + +
1174D GLU* 5.4 9.6 + - - +
1175D PHE* 3.5 31.5 - - + -
1185D GLU 3.0 17.2 + - - +
1186D PHE 4.4 0.2 - - - +
1188D ALA* 1.3 79.3 - - - +
1190D ASN* 1.3 56.3 - - - +
1191D ARG 3.0 4.9 - - - -
1192D ARG* 3.0 43.4 + - - +
1193D VAL* 3.0 36.6 + - - +
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Residues in contact with ASN1190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173D THR* 3.4 15.9 - - - +
1175D PHE* 5.1 0.5 - - - -
1186D PHE* 3.2 35.4 + - + +
1187D GLU* 4.3 5.6 - - - -
1189D GLU* 1.3 75.9 - - - +
1191D ARG* 1.3 58.5 + - - +
1192D ARG 3.4 0.2 - - - -
1193D VAL* 4.6 2.2 - - - +
1194D VAL* 3.1 31.7 - - - +
1200D PRO* 3.4 15.0 - - + +
1201D ALA* 3.0 47.3 + - - +
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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