Contacts of the helix formed by residues 1124 - 1141 (chain B) in PDB entry 5W0N
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 ASN1124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B PHE* 3.8 10.5 - - + -
1062B CYS* 3.5 17.0 - - + +
1104B VAL* 3.7 27.6 - - + +
1121B SER* 3.5 28.4 + - - +
1122B LEU 3.1 2.6 + - - +
1123B TYR* 1.3 72.2 - - - +
1125B THR* 1.3 63.0 + - - +
1126B LEU* 3.4 2.3 + - - +
1127B ALA* 3.1 35.0 + - + +
1128B LEU* 3.4 15.6 + - - +
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Residues in contact with THR1125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B CYS* 5.5 0.2 - - - -
1123B TYR* 3.0 23.2 + - - +
1124B ASN* 1.3 73.0 - - - +
1126B LEU* 1.3 64.1 + - - +
1128B LEU* 3.1 26.3 + - + +
1129B HIS* 3.0 30.7 + - + -
1206B VAL* 3.4 29.8 - - + -
1207B ASP* 3.7 11.4 + - - -
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Residues in contact with LEU1126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124B ASN* 3.4 2.6 + - - +
1125B THR* 1.3 77.0 - - - +
1127B ALA* 1.3 62.8 + - - +
1129B HIS* 3.0 6.4 + - - +
1130B ASN* 3.0 28.2 + - - +
1206B VAL* 3.5 28.5 - - + +
1207B ASP* 4.5 14.5 + - + +
1209B TRP* 3.9 28.7 - - + +
1211B ILE* 3.6 26.0 - - + -
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Residues in contact with ALA1127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B PHE* 3.6 24.7 - - + -
1124B ASN* 3.1 34.3 + - - +
1125B THR 3.2 0.4 - - - -
1126B LEU* 1.3 78.3 - - - +
1128B LEU* 1.3 56.7 + - - +
1130B ASN* 3.1 15.7 - - - +
1131B THR* 2.7 35.5 + - - -
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Residues in contact with LEU1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043B SER* 4.0 27.8 - - - +
1044B LEU 4.0 5.2 - - - +
1045B PHE* 3.9 20.4 - - + -
1062B CYS* 4.0 27.4 - - + -
1064B THR* 6.0 2.2 - - + -
1124B ASN 3.4 9.4 + - - +
1125B THR* 3.1 19.6 + - + +
1127B ALA* 1.3 79.9 - - - +
1129B HIS* 1.3 63.6 - - + +
1131B THR* 3.5 7.0 - - - -
1132B ARG* 3.3 27.4 + - - +
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Residues in contact with HIS1129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125B THR* 3.0 41.8 + - + +
1126B LEU* 3.0 9.6 + - - +
1128B LEU* 1.3 78.9 - - + +
1130B ASN* 1.3 60.8 + - - +
1131B THR 3.2 1.6 - - - -
1132B ARG* 3.1 35.4 + - - +
1133B LEU* 2.9 26.2 + - - +
1206B VAL* 4.0 15.7 - - + +
1211B ILE* 3.6 44.2 - - + +
1213B PHE* 4.0 4.8 - - + -
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Residues in contact with ASN1130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126B LEU* 3.0 12.6 + - - +
1127B ALA* 3.1 29.2 - - - +
1129B HIS* 1.3 73.9 - - - +
1131B THR* 1.3 67.6 + - - +
1133B LEU* 3.6 14.8 - - + -
1134B LEU* 2.9 36.4 + - + +
1171B TYR* 3.3 44.6 + - + +
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Residues in contact with THR1131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044B LEU 5.3 0.2 - - - +
1045B PHE* 3.5 8.4 - - + +
1046B GLY* 3.1 35.0 + - - +
1049B LYS* 3.7 31.6 - - + +
1050B ASN* 3.7 13.8 + - + +
1127B ALA 2.7 20.6 + - - -
1128B LEU* 3.5 7.4 - - - +
1129B HIS 3.2 0.2 - - - -
1130B ASN* 1.3 83.2 + - - +
1132B ARG* 1.3 67.1 + - + +
1134B LEU* 3.4 0.9 + - - -
1135B SER* 2.9 23.0 + - - -
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Residues in contact with ARG1132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128B LEU* 3.3 13.6 + - - +
1129B HIS* 3.1 39.3 + - - +
1131B THR* 1.3 79.5 - - + +
1133B LEU* 1.3 61.8 + - - +
1135B SER* 3.3 7.4 + - - -
1136B ALA* 3.0 23.4 + - - +
1211B ILE* 5.1 2.6 - - - +
1213B PHE* 3.7 30.0 + - + -
1215B ASP* 3.7 22.0 + - - +
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Residues in contact with LEU1133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129B HIS 2.9 16.9 + - - +
1130B ASN* 3.6 13.9 - - + +
1131B THR 3.2 0.2 - - - -
1132B ARG* 1.3 76.4 - - - +
1134B LEU* 1.3 72.6 + - + +
1136B ALA* 3.1 6.1 + - - +
1137B TYR* 3.1 52.4 + - + -
1175B LEU* 6.2 2.2 - - + -
1192B LEU* 4.5 3.8 - - + -
1193B GLN* 3.9 26.2 - - + +
1213B PHE* 3.4 46.8 - - + -
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Residues in contact with LEU1134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050B ASN* 3.7 32.7 - - + +
1052B PHE* 3.9 6.9 - - + -
1130B ASN* 2.9 23.5 + - + +
1131B THR* 5.7 0.2 - - - -
1133B LEU* 1.3 89.3 - - + +
1135B SER* 1.3 57.7 + - - +
1137B TYR* 3.2 7.8 + - - +
1138B SER* 2.9 28.8 + - - -
1171B TYR* 3.9 30.7 - - + +
1174B THR* 3.5 27.4 - - + -
1175B LEU* 4.5 8.7 - - + -
1178B LEU* 3.9 24.7 - - + -
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Residues in contact with SER1135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049B LYS 3.7 19.6 + - - -
1050B ASN* 3.5 12.3 + - - -
1051B GLY* 5.5 0.5 - - - -
1131B THR 2.9 18.7 + - - -
1132B ARG* 3.6 9.0 - - - -
1134B LEU* 1.3 76.8 - - - +
1136B ALA* 1.3 61.8 + - - +
1138B SER* 2.8 20.6 + - - -
1139B ALA* 3.2 10.2 + - - +
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Residues in contact with ALA1136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132B ARG 3.0 13.1 + - - +
1133B LEU 3.1 9.6 + - - +
1135B SER* 1.3 76.6 - - - +
1137B TYR* 1.3 61.8 + - - +
1139B ALA* 3.1 14.5 + - - +
1140B ILE* 3.4 17.2 + - - +
1192B LEU* 3.8 17.0 - - + -
1213B PHE* 4.0 14.1 - - + -
1214B PHE 4.8 0.4 - - - +
1215B ASP* 4.9 3.8 - - + -
1217B ILE* 4.0 19.4 - - + +
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Residues in contact with TYR1137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133B LEU* 3.1 52.4 + - + +
1134B LEU* 3.5 6.7 - - - +
1136B ALA* 1.3 76.0 - - - +
1138B SER* 1.3 64.7 + - - +
1139B ALA 3.1 0.9 + - - -
1140B ILE* 3.1 27.0 + - + +
1144B VAL* 3.6 15.5 - - + +
1178B LEU* 3.9 36.6 - - + -
1182B GLN* 3.0 24.4 + - - -
1189B ILE* 3.7 19.0 - - + +
1190B PRO 3.3 20.2 - - - -
1191B VAL* 3.8 1.7 - - - +
1192B LEU* 3.0 38.2 + - + +
1193B GLN* 4.4 6.3 + - - -
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Residues in contact with SER1138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050B ASN 3.8 5.6 + - - -
1051B GLY* 4.2 2.3 - - - -
1052B PHE* 3.4 30.7 - - - -
1134B LEU 2.9 9.3 + - - -
1135B SER* 2.8 19.8 + - - -
1137B TYR* 1.3 75.6 - - - +
1139B ALA* 1.3 58.9 + - - +
1141B ASP 3.6 15.2 + - - +
1142B PRO* 5.0 1.0 - - - +
1144B VAL* 3.8 11.6 - - - +
1145B LYS* 4.0 30.6 - - - +
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Residues in contact with ALA1139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135B SER 3.7 8.1 - - - +
1136B ALA* 3.1 12.5 + - - +
1137B TYR 3.1 1.0 - - - -
1138B SER* 1.3 79.9 + - - +
1140B ILE* 1.3 63.7 + - - +
1141B ASP* 3.3 1.7 + - - -
1142B PRO* 5.9 0.2 - - - +
1217B ILE* 4.4 15.0 - - + +
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Residues in contact with ILE1140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136B ALA 3.4 15.9 - - - +
1137B TYR* 3.1 24.1 + - + +
1139B ALA* 1.3 79.9 - - - +
1141B ASP* 1.3 61.0 + - + +
1142B PRO* 4.8 0.5 - - - +
1188B VAL 4.4 8.3 - - - +
1189B ILE* 4.1 15.9 - - + -
1190B PRO* 3.7 26.0 - - + -
1192B LEU* 4.0 17.5 - - + -
1217B ILE* 3.8 20.4 - - + -
1220B LEU* 3.9 21.5 - - + -
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Residues in contact with ASP1141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137B TYR 4.1 1.4 + - - -
1138B SER 3.6 8.2 - - - +
1139B ALA 3.3 1.9 - - - -
1140B ILE* 1.3 88.4 - - + +
1142B PRO* 1.3 79.3 - - - +
1143B ARG* 2.8 66.9 + - - +
1144B VAL* 2.9 32.0 + - + +
1145B LYS 4.0 0.2 + - - -
1188B VAL* 4.3 10.6 - - + +
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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