Contacts of the helix formed by residues 1144 - 1157 (chain A) in PDB entry 5LUQ
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 SER1144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1142A HIS 2.3 24.4 + - - -
1143A VAL* 1.3 67.2 + - - +
1145A LEU* 1.3 61.6 + - - -
1146A ASN 3.1 1.6 - - - +
1147A LYS* 3.3 44.2 + - - +
1148A ALA* 3.8 4.9 + - - +
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Residues in contact with LEU1145 (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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1102A GLU* 4.9 13.2 - - + -
1143A VAL* 2.8 33.3 + - + +
1144A SER* 1.3 70.7 - - - +
1146A ASN* 1.3 70.0 + - - +
1148A ALA* 3.7 5.2 - - - +
1149A LYS* 2.9 74.9 + - + +
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Residues in contact with ASN1146 (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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1098A GLN* 4.1 4.7 + - - +
1102A GLU* 3.1 23.1 - - - +
1138A ILE* 4.6 13.0 + - + +
1141A LYS* 5.6 0.6 - - - +
1142A HIS* 2.6 39.9 + - - +
1143A VAL* 3.1 17.5 - - - +
1145A LEU* 1.3 75.5 - - - +
1147A LYS* 1.3 64.3 + - + +
1148A ALA 2.9 5.4 + - - -
1150A LYS* 2.8 40.7 + - + +
1151A ARG* 2.9 9.5 + - - +
1180A GLN* 4.9 4.8 + - - +
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Residues in contact with LYS1147 (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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1141A LYS* 3.9 30.4 - - - +
1142A HIS 5.3 2.5 - - - +
1144A SER* 3.3 35.9 + - - +
1146A ASN* 1.3 77.5 - - + +
1148A ALA* 1.3 56.4 + - - +
1151A ARG* 2.5 38.5 + - - +
1179A PRO 5.0 0.6 + - - -
1180A GLN* 3.3 48.4 - - + +
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Residues in contact with ALA1148 (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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1144A SER 4.5 3.8 - - - +
1145A LEU* 3.2 11.2 + - - +
1146A ASN 2.9 1.6 + - - -
1147A LYS* 1.3 79.0 - - + +
1149A LYS* 1.3 69.4 + - + +
1151A ARG* 3.4 9.9 + - - +
1152A ARG* 2.9 41.1 + - - +
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Residues in contact with LYS1149 (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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1102A GLU* 5.0 3.1 - - - +
1145A LEU* 2.9 67.8 + - + +
1148A ALA* 1.3 82.6 - - + +
1150A LYS* 1.3 55.1 + - - +
1152A ARG* 2.8 36.1 + - - +
1153A LEU* 3.1 12.0 + - - +
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Residues in contact with LYS1150 (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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1101A PHE 2.8 25.2 + - - -
1102A GLU* 2.8 51.6 + - - +
1105A VAL* 3.3 13.1 - - + +
1138A ILE* 3.3 44.4 - - + -
1139A GLU* 5.1 6.1 - - - +
1145A LEU 3.7 1.6 + - - -
1146A ASN* 2.8 29.2 + - + +
1149A LYS* 1.3 77.9 - - - +
1151A ARG* 1.3 55.9 + - - +
1153A LEU* 3.8 6.4 + - - +
1154A PRO* 2.9 23.4 - - - +
1176A CYS* 5.2 6.3 - - - +
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Residues in contact with ARG1151 (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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1146A ASN 2.9 5.6 + - - +
1147A LYS* 2.5 39.8 + - - +
1148A ALA* 4.3 8.8 + - - +
1149A LYS 3.1 0.6 - - - -
1150A LYS* 1.3 74.4 - - - +
1152A ARG* 1.3 67.8 + - - +
1153A LEU 3.2 1.8 - - - -
1154A PRO* 3.1 13.9 - - - +
1155A ARG* 3.5 11.0 + - + +
1176A CYS* 4.3 25.4 - - + +
1177A GLY* 4.7 8.7 - - - +
1180A GLN* 4.5 22.1 + - - +
1219A PHE* 4.2 27.6 - - + -
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Residues in contact with ARG1152 (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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1148A ALA* 2.9 31.9 + - - +
1149A LYS* 2.8 25.4 + - - +
1151A ARG* 1.3 75.2 - - - +
1153A LEU* 1.3 54.9 + - - +
1155A ARG* 3.1 11.6 + - - +
1156A GLY* 2.8 24.6 + - - -
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Residues in contact with LEU1153 (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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1105A VAL* 3.4 44.2 - - + -
1109A GLU* 6.1 0.9 - - + -
1149A LYS 3.1 9.6 + - - +
1150A LYS* 4.0 7.6 - - - +
1152A ARG* 1.3 75.2 - - - +
1154A PRO* 1.3 68.0 - - + +
1156A GLY* 2.7 23.3 + - - +
1157A PHE* 3.0 55.2 + - + -
1172A LEU* 4.7 3.4 - - + -
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Residues in contact with PRO1154 (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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1150A LYS 2.9 29.2 - - - +
1151A ARG 3.1 13.0 - - - +
1153A LEU* 1.3 82.8 - - + +
1155A ARG* 1.3 60.2 + - - +
1157A PHE* 3.2 14.7 + - + +
1158A PRO* 3.0 19.8 - - - +
1169A VAL 5.4 0.4 - - - +
1172A LEU* 3.8 43.5 - - + +
1173A LEU* 3.3 16.2 - - + +
1176A CYS* 4.2 18.6 - - + -
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Residues in contact with ARG1155 (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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1151A ARG* 3.5 9.8 + - + +
1152A ARG* 3.1 13.8 + - - +
1154A PRO* 1.3 78.3 - - - +
1156A GLY* 1.3 56.9 + - - +
1157A PHE 3.0 5.1 + - - -
1158A PRO* 3.0 12.8 - - - +
1159A PRO* 3.0 33.4 - - - +
1173A LEU* 4.0 12.2 - - + +
1219A PHE* 3.7 39.5 - - + -
1223A THR* 5.6 3.0 - - - +
1230A GLY 3.1 26.3 + - - -
1231A GLN* 3.9 18.7 - - - +
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Residues in contact with GLY1156 (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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1152A ARG 2.8 10.1 + - - -
1153A LEU* 2.7 15.7 + - - -
1155A ARG* 1.3 74.0 - - - +
1157A PHE* 1.3 59.5 + - - -
1158A PRO 3.7 0.2 - - - -
1159A PRO* 3.6 13.0 - - - +
1160A SER* 2.8 19.6 + - - -
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Residues in contact with PHE1157 (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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1105A VAL 4.2 1.6 - - - -
1108A MSE 3.5 25.6 - - - -
1109A GLU* 4.0 36.6 - - + -
1153A LEU* 3.0 53.7 + - + -
1154A PRO* 3.4 13.7 - - + +
1155A ARG 3.0 2.4 + - - -
1156A GLY* 1.3 82.1 - - - +
1158A PRO* 1.3 61.8 - - + +
1159A PRO 3.5 0.2 - - - -
1160A SER* 2.9 35.7 - - - +
1161A ALA* 3.1 6.9 + - - +
1165A LEU* 4.8 3.4 - - + -
1169A VAL* 3.7 26.3 - - + +
1172A LEU* 3.8 16.8 - - + -
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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