Contacts of the strand formed by residues 1156 - 1166 (chain A) in PDB entry 3E0D
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 PRO1156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1152A LEU 4.4 1.5 - - - +
1153A ASP 4.2 7.9 - - - +
1154A GLU 3.6 8.7 - - - +
1155A HIS* 1.3 91.8 - - - +
1157A GLY* 1.3 58.6 + - - +
1179A VAL* 6.2 0.9 - - + -
1180A ARG 3.3 7.6 - - - +
1182A GLY* 3.5 9.3 - - - -
1184A GLU* 4.4 5.5 - - - +
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Residues in contact with GLY1157 (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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1156A PRO* 1.3 77.1 - - - +
1158A SER* 1.3 63.9 + - - -
1180A ARG* 2.7 22.0 + - - +
1181A VAL 3.7 5.2 - - - -
1182A GLY* 3.7 5.8 - - - -
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Residues in contact with SER1158 (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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1157A GLY* 1.3 75.6 - - - -
1159A LEU* 1.3 70.2 + - - +
1160A PRO* 3.7 2.6 - - - +
1180A ARG* 3.4 31.4 + - - +
1181A VAL 3.2 2.2 + - - -
1182A GLY* 4.5 1.0 - - - -
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Residues in contact with LEU1159 (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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1129A LYS 5.6 0.4 - - - +
1130A ALA* 3.9 20.9 - - + -
1131A LEU* 4.2 8.3 - - + +
1158A SER* 1.3 84.0 - - - +
1160A PRO* 1.3 70.6 - - + +
1161A VAL* 3.7 1.2 + - - +
1180A ARG* 3.3 5.9 - - - -
1181A VAL* 2.8 41.8 + - + +
1182A GLY* 4.7 0.9 - - - -
1183A GLU* 3.5 45.1 - - + +
1198A LEU* 3.8 24.5 - - + -
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Residues in contact with PRO1160 (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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1130A ALA* 3.6 17.3 - - + +
1131A LEU 3.3 21.3 + - - +
1158A SER 3.7 2.2 - - - +
1159A LEU* 1.3 86.5 - - - +
1161A VAL* 1.3 61.7 + - - +
1162A TYR* 3.8 19.0 - - + +
1179A VAL 4.9 3.4 - - - +
1180A ARG* 3.4 33.6 - - - +
1201A ASP* 3.4 26.2 - - - +
1203A GLU* 5.2 5.2 - - + -
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Residues in contact with VAL1161 (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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1131A LEU* 3.3 13.5 - - + +
1133A VAL* 4.2 13.7 - - + -
1152A LEU* 3.8 22.0 - - + -
1159A LEU 4.1 3.1 - - - +
1160A PRO* 1.3 76.5 - - - +
1162A TYR* 1.3 68.7 + - - +
1163A LEU* 4.8 4.7 - - + -
1175A ALA* 3.5 2.4 - - - +
1176A LEU* 2.7 56.9 + - + +
1179A VAL* 4.4 8.3 + - + +
1181A VAL* 3.8 36.8 - - + +
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Residues in contact with TYR1162 (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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1130A ALA* 4.1 15.9 - - + -
1131A LEU 3.0 6.9 + - - +
1132A GLU* 3.8 23.3 - - + +
1133A VAL 3.0 23.7 + - - -
1160A PRO* 3.8 29.6 - - + +
1161A VAL* 1.3 79.4 - - - +
1163A LEU* 1.3 68.5 + - - +
1173A LEU* 5.0 8.5 - - + -
1174A PHE 3.8 2.7 - - - -
1175A ALA* 3.8 26.2 - - + -
1199A VAL* 5.1 5.8 - - + -
1200A PRO 5.6 0.2 - - - -
1201A ASP* 2.6 29.4 + - - -
1202A ARG* 3.5 45.1 + - + +
1203A GLU* 3.9 12.5 + - - +
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Residues in contact with LEU1163 (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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1133A VAL* 3.4 25.8 - - + -
1135A VAL* 3.8 17.9 - - + -
1148A LEU* 3.9 18.6 - - + -
1152A LEU* 5.9 0.2 - - + -
1161A VAL* 4.8 4.7 - - + -
1162A TYR* 1.3 83.3 - - - +
1164A ARG* 1.3 63.6 + - - +
1165A VAL* 3.6 14.8 + - + +
1172A ALA 3.6 0.5 - - - +
1173A LEU* 3.6 7.6 - - - +
1174A PHE* 2.8 48.7 + - + +
1176A LEU* 3.7 29.4 - - + -
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Residues in contact with ARG1164 (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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1022A ARG 4.2 4.6 + - - -
1023A GLU* 3.3 21.0 + - - +
1024A VAL 4.7 0.2 + - - -
1025A ALA 2.7 27.9 + - - -
1026A SER 4.5 3.8 - - - -
1027A CYS* 4.9 0.6 - - - +
1132A GLU* 3.2 32.8 + - - +
1133A VAL 3.1 6.3 + - - -
1134A GLU* 3.7 32.7 + - + +
1135A VAL* 2.9 28.1 + - - +
1163A LEU* 1.3 72.4 - - - +
1165A VAL* 1.3 61.6 + - - +
1166A LEU* 3.6 5.1 + - + +
1171A GLU* 3.5 34.5 + - + +
1172A ALA 3.7 4.9 - - - +
1173A LEU* 3.5 32.6 - - + +
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Residues in contact with VAL1165 (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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1135A VAL* 3.6 7.2 - - + +
1136A ASP 4.5 15.3 - - - +
1137A HIS* 5.2 6.3 - - - +
1139A LEU* 4.8 12.3 - - + -
1163A LEU* 4.1 19.1 - - + +
1164A ARG* 1.3 74.4 - - - +
1166A LEU* 1.3 57.0 + - - +
1167A GLY* 2.8 19.8 + - - +
1171A GLU* 4.7 2.4 - - - +
1172A ALA* 3.2 31.9 + - + +
1174A PHE* 3.7 31.2 - - + -
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Residues in contact with LEU1166 (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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1031A GLU* 5.7 2.5 - - - +
1134A GLU* 5.6 7.6 - - + +
1135A VAL 3.4 13.5 + - - +
1136A ASP* 4.3 19.3 - - - +
1137A HIS* 3.5 24.6 + - - +
1164A ARG* 3.7 4.7 - - + +
1165A VAL* 1.3 67.7 - - - +
1167A GLY* 1.3 65.4 + - - +
1170A GLY 4.6 0.4 - - - -
1171A GLU* 3.8 33.0 - - + +
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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