Contacts of the helix formed by residues 1126 - 1140 (chain A) in PDB entry 4N78
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 GLU1126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953A MET* 4.1 8.6 - - - +
1109A TRP 3.8 4.0 - - - -
1110A ARG* 3.3 22.5 - - - +
1120A HIS* 3.6 35.2 + - + +
1125A VAL* 1.3 83.6 - - + +
1127A PHE* 1.3 66.4 + - - +
1128A HIS* 2.9 35.5 + - + +
1129A ARG* 3.2 21.8 + - + +
1130A LEU 3.5 2.9 + - - -
1170A GLN* 3.9 6.9 + - - +
1173A ARG* 3.0 35.4 + - - -
1177A LEU* 5.9 0.2 - - - +
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Residues in contact with PHE1127 (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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945A ILE* 6.0 0.4 - - + -
949A VAL* 4.3 14.6 - - + -
953A MET* 4.5 4.7 - - - +
997A LEU* 5.4 4.7 - - + -
1108A ILE 4.9 0.8 + - - -
1109A TRP* 3.1 45.3 + + + +
1126A GLU* 1.3 73.1 - - - +
1128A HIS* 1.3 60.4 + - - +
1130A LEU* 2.8 42.7 + - + +
1131A TRP* 2.9 36.8 + + + -
1134A MET* 5.6 3.6 - - + -
1161A GLY* 3.8 14.6 - - - -
1164A ILE* 3.5 43.7 - - + -
1165A ILE* 3.9 13.0 - - + -
1168A LEU* 3.9 14.1 - - + -
1170A GLN* 3.6 0.8 + - - -
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Residues in contact with HIS1128 (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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1126A GLU* 2.9 30.6 + - + -
1127A PHE* 1.3 76.1 - - - +
1129A ARG* 1.3 84.8 + - - +
1131A TRP* 3.3 10.6 + - - +
1132A SER* 2.9 31.0 + - - -
1165A ILE* 3.9 15.3 - - + -
1170A GLN* 3.0 40.6 + - + +
1173A ARG* 3.9 26.7 - - + +
1174A PHE* 3.6 33.3 - - + -
1177A LEU* 4.2 11.7 - - + +
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Residues in contact with ARG1129 (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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956A MET* 3.2 12.3 - - + +
960A CYS 3.0 26.5 + - - -
962A LEU* 5.1 3.4 - - - +
1121A VAL 4.1 9.3 + - - -
1122A ASP 4.1 4.9 + - - -
1123A GLU 3.7 19.7 + - - +
1124A CYS* 3.9 29.0 - - + -
1126A GLU* 3.3 16.6 - - + +
1127A PHE 2.9 0.8 + - - -
1128A HIS* 1.3 101.5 - - + +
1130A LEU* 1.3 64.1 + - - +
1132A SER* 3.0 17.0 + - - -
1133A ALA 3.1 10.2 + - - -
1177A LEU* 2.5 47.1 + - - +
1178A ASP* 4.8 0.6 - - - +
1179A PHE* 3.3 27.3 - - - -
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Residues in contact with LEU1130 (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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949A VAL* 4.1 34.5 - - + +
952A LEU* 3.9 24.2 - - + +
953A MET* 3.6 30.4 - - + +
956A MET* 3.9 22.4 - - - +
983A ILE* 4.4 7.4 - - + -
1126A GLU 3.5 1.8 + - - -
1127A PHE* 2.8 19.8 + - + +
1129A ARG* 1.3 74.4 - - - +
1131A TRP* 1.3 56.9 + - - +
1133A ALA* 3.2 2.9 + - + +
1134A MET* 3.0 52.6 + - + +
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Residues in contact with TRP1131 (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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994A PHE* 5.1 0.9 - + - -
997A LEU* 3.5 25.4 - - + -
1127A PHE* 2.9 25.4 + + + +
1128A HIS* 3.5 12.8 - - - +
1129A ARG 3.1 0.2 - - - -
1130A LEU* 1.3 75.9 - - - +
1132A SER* 1.3 54.3 + - - +
1134A MET* 3.2 25.4 + - + +
1135A GLN* 2.7 34.1 + - + +
1138A TYR* 4.1 29.2 + + - -
1157A LEU* 3.5 37.2 - - + -
1158A HIS* 4.2 11.2 - - + -
1161A GLY* 3.6 25.4 - - - -
1162A CYS* 4.7 7.9 - - - +
1165A ILE* 3.5 25.0 - - + +
1174A PHE* 3.7 18.2 - + - -
1215A ASN* 4.9 2.6 - - - +
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Residues in contact with SER1132 (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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1128A HIS* 2.9 22.2 + - - -
1129A ARG* 3.0 13.1 + - - -
1131A TRP* 1.3 77.4 - - - +
1133A ALA* 1.3 57.6 + - - +
1135A GLN* 3.3 3.8 + - - +
1136A PHE* 2.9 27.5 + - - +
1174A PHE* 3.4 10.4 - - - -
1177A LEU 4.8 0.9 + - - -
1178A ASP* 3.0 34.4 + - - +
1179A PHE* 3.4 26.8 - - - +
1180A CYS* 4.8 1.7 - - - -
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Residues in contact with ALA1133 (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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956A MET* 3.4 31.4 - - + -
980A LEU* 4.0 24.1 - - + +
983A ILE* 4.0 18.0 - - + +
1129A ARG 3.1 5.7 + - - -
1130A LEU* 3.4 9.4 - - + +
1131A TRP 3.2 0.2 - - - -
1132A SER* 1.3 74.1 - - - +
1134A MET* 1.3 64.5 + - - +
1136A PHE* 3.2 6.1 + - - +
1137A VAL* 3.1 23.9 + - - +
1179A PHE* 3.8 0.8 - - - -
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Residues in contact with MET1134 (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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949A VAL* 5.8 3.4 - - + -
952A LEU* 3.6 30.7 - - + -
983A ILE* 4.9 3.4 - - + -
989A LEU* 4.1 13.9 - - + -
993A CYS* 4.5 10.1 - - + -
994A PHE* 4.0 24.3 - - + -
997A LEU* 4.5 7.0 - - + -
1127A PHE* 5.6 4.0 - - + -
1130A LEU* 3.0 38.9 + - + +
1131A TRP* 3.2 39.2 + - + +
1133A ALA* 1.3 75.5 - - - +
1135A GLN* 1.3 62.4 + - - +
1137A VAL* 3.1 19.7 + - - +
1138A TYR* 3.1 19.0 + - + +
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Residues in contact with GLN1135 (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 TRP* 2.7 21.7 + - + +
1132A SER* 3.5 4.7 - - - +
1133A ALA 3.2 0.2 - - - -
1134A MET* 1.3 69.8 - - - +
1136A PHE* 1.3 65.9 + - - +
1138A TYR* 3.0 32.4 + - + +
1139A CYS* 3.0 42.0 + - - -
1174A PHE* 3.7 9.6 - - - -
1178A ASP* 2.8 41.4 + - - -
1180A CYS* 4.1 5.7 - - - +
1181A TYR* 3.8 10.8 + - - -
1208A ILE* 5.9 0.4 - - - -
1211A PHE* 4.1 6.5 - - - +
1215A ASN* 2.5 32.0 + - - -
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Residues in contact with PHE1136 (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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973A LEU* 4.0 9.2 - - + -
976A PHE* 3.8 27.8 - + + -
977A HIS* 3.8 48.9 - + - -
980A LEU* 3.7 21.3 - - + -
984A VAL* 3.9 26.5 - - + -
1132A SER 2.9 13.1 + - - +
1133A ALA 3.2 10.7 + - - +
1135A GLN* 1.3 77.0 - - - +
1137A VAL* 1.3 64.4 + - - +
1139A CYS 3.6 0.3 + - - -
1140A ILE* 3.2 30.8 + - + +
1179A PHE* 5.2 2.9 - - + -
1180A CYS* 3.4 18.8 - - - -
1183A LEU* 5.3 1.6 - - + -
1204A MET* 3.7 27.8 - - + +
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Residues in contact with VAL1137 (chain A).
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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980A LEU* 6.3 0.2 - - + -
983A ILE* 4.0 7.0 - - + -
984A VAL* 4.0 34.5 - - + +
989A LEU* 3.8 31.9 - - + -
990A LYS* 4.2 22.8 - - - +
994A PHE* 4.8 3.6 - - + -
1133A ALA 3.1 13.9 + - - +
1134A MET* 3.1 8.4 + - - +
1136A PHE* 1.3 77.6 - - + +
1138A TYR* 1.3 58.9 + - - +
1139A CYS 3.2 0.2 - - - -
1140A ILE* 3.2 33.3 + - + +
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Residues in contact with TYR1138 (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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990A LYS* 6.0 2.9 - - - +
994A PHE* 4.2 18.8 - + + -
1131A TRP* 4.1 24.0 + + - -
1134A MET* 3.1 20.1 + - + -
1135A GLN* 3.0 50.8 + - + +
1137A VAL* 1.3 77.4 - - - +
1139A CYS* 1.3 61.4 + - - +
1140A ILE 3.3 3.0 - - - +
1149A VAL* 3.7 27.6 - - + +
1157A LEU* 4.6 4.5 - - + -
1158A HIS* 3.5 25.3 + + - -
1207A ARG* 3.0 24.4 + - - -
1211A PHE* 3.5 40.2 - + - -
1215A ASN* 4.1 2.9 + - - -
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Residues in contact with CYS1139 (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 GLN* 3.0 41.7 + - - +
1136A PHE 3.9 4.5 - - - +
1137A VAL 3.2 0.4 - - - -
1138A TYR* 1.3 78.6 - - - +
1140A ILE* 1.3 65.0 + - - +
1141A PRO* 3.2 6.2 - - - +
1180A CYS* 4.1 2.5 - - - -
1204A MET* 3.5 10.8 - - + +
1207A ARG* 3.1 24.7 + - - +
1208A ILE* 3.8 37.2 - - + +
1211A PHE* 3.8 24.0 - - - -
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Residues in contact with ILE1140 (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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977A HIS* 4.0 25.1 - - + -
984A VAL* 4.6 14.1 - - + -
1136A PHE* 3.2 29.6 - - + +
1137A VAL* 3.2 19.0 + - + +
1138A TYR 4.4 2.9 - - - +
1139A CYS* 1.3 77.5 - - - +
1141A PRO* 1.3 84.3 - - + +
1142A VAL* 3.6 12.1 + - + +
1199A VAL* 4.0 18.2 - - + -
1204A MET* 3.8 12.3 - - + -
1207A ARG* 4.3 4.6 + - - -
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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