Contacts of the helix formed by residues 1120 - 1134 (chain A) in PDB entry 1N35
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 ASP1120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007A PRO* 6.1 0.6 - - - +
1015A LYS* 4.7 8.3 - - - +
1115A THR* 4.6 0.4 - - - -
1118A GLY 4.3 0.2 + - - -
1119A LEU* 1.3 74.6 - - - +
1121A VAL* 1.3 63.1 + - - +
1122A ASN* 2.9 25.9 + - - +
1123A ALA* 2.8 41.6 + - + +
1124A ILE* 2.8 18.5 + - - +
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Residues in contact with VAL1121 (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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1110A LEU* 4.4 12.2 - - + +
1112A MET* 2.8 35.0 - - + +
1113A ALA 3.6 23.3 - - - +
1114A LYS* 4.3 8.3 - - - +
1115A THR* 4.1 19.2 - - + +
1119A LEU 3.9 2.4 + - - +
1120A ASP* 1.3 74.6 + - - +
1122A ASN* 1.3 63.7 + - - +
1124A ILE* 3.3 9.3 + - + +
1125A ASP* 3.0 23.1 + - - +
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Residues in contact with ASN1122 (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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1110A LEU* 3.3 27.0 - - - +
1120A ASP* 2.9 16.4 + - - +
1121A VAL* 1.3 79.2 - - - +
1123A ALA* 1.3 58.2 + - - +
1125A ASP* 3.6 6.8 + - - +
1126A SER* 3.1 27.2 + - - -
1174A ARG* 3.6 29.4 + - - +
1290C C 4.7 12.9 + - - -
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Residues in contact with ALA1123 (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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1007A PRO* 4.2 13.9 - - + +
1015A LYS* 5.9 2.5 - - - +
1120A ASP* 2.8 31.4 + - + +
1122A ASN* 1.3 78.0 - - - +
1124A ILE* 1.3 64.4 + - - +
1126A SER* 3.1 7.6 + - - -
1127A ALA* 3.0 23.6 + - - +
1130A ARG* 5.2 1.6 + - - -
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Residues in contact with ILE1124 (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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1007A PRO* 3.9 23.8 - - + -
1112A MET* 4.6 20.2 - - + -
1115A THR* 3.7 31.0 - - + +
1119A LEU* 4.4 6.5 - - + -
1120A ASP 2.8 17.6 + - - +
1121A VAL* 3.3 8.9 + - + +
1123A ALA* 1.3 74.8 - - - +
1125A ASP* 1.3 63.2 + - - +
1127A ALA* 3.4 2.3 + - - +
1128A LEU* 3.2 40.2 + - + +
1144A GLN* 5.1 5.4 - - + -
1145A LEU* 5.0 1.6 - - + -
1148A VAL* 3.5 35.2 - - + -
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Residues in contact with ASP1125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1110A LEU* 3.8 17.3 - - + -
1111A PHE* 3.1 27.0 + - - +
1112A MET 4.9 0.6 + - - +
1121A VAL 3.0 16.8 + - - +
1122A ASN* 3.8 5.8 - - - +
1124A ILE* 1.3 77.0 - - - +
1126A SER* 1.3 62.7 + - - +
1128A LEU* 3.6 8.5 + - - +
1129A LEU* 3.2 54.1 + - - +
1171A GLN* 3.0 32.9 + - - +
1174A ARG* 3.6 9.0 + - - +
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Residues in contact with SER1126 (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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1122A ASN 3.1 18.4 + - - -
1123A ALA* 3.1 7.8 + - - -
1125A ASP* 1.3 76.0 + - - +
1127A ALA* 1.3 60.3 + - - +
1129A LEU* 3.5 3.8 + - - +
1130A ARG* 2.8 54.2 + - - +
1174A ARG* 3.2 34.7 + - - +
1175A VAL 4.5 0.2 - - - -
1177A ASN* 4.5 6.7 + - - -
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Residues in contact with ALA1127 (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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1003A ILE* 3.8 19.2 - - + +
1007A PRO* 3.8 22.7 - - + -
1123A ALA 3.0 15.0 + - - +
1124A ILE 3.7 4.9 - - - +
1126A SER* 1.3 75.8 - - - +
1128A LEU* 1.3 59.3 - - - +
1130A ARG* 3.3 17.5 + - - +
1131A LEU* 2.9 36.8 + - - +
1144A GLN* 3.8 7.0 - - - +
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Residues in contact with LEU1128 (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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1111A PHE* 4.5 10.8 - - + -
1112A MET* 5.5 1.8 - - + -
1124A ILE* 3.2 36.2 + - + +
1125A ASP* 3.9 8.1 - - - +
1126A SER 3.3 0.2 - - - -
1127A ALA* 1.3 77.6 - - - +
1129A LEU* 1.3 61.9 + - - +
1131A LEU* 3.5 5.1 + - - +
1132A ARG* 3.1 18.5 + - - +
1141A LEU* 3.6 45.2 - - + +
1144A GLN* 3.9 22.9 - - + -
1145A LEU* 3.9 20.6 - - + -
1158A LEU* 5.3 0.2 - - + -
1162A ILE* 4.0 27.1 - - + -
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Residues in contact with LEU1129 (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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1111A PHE* 4.0 15.5 - - + -
1125A ASP* 3.2 39.9 + - - +
1126A SER* 4.1 2.7 - - - +
1128A LEU* 1.3 76.9 - - - +
1130A ARG* 1.3 61.7 + - - +
1132A ARG* 3.2 16.6 + - - +
1133A THR* 2.7 34.7 + - - -
1162A ILE* 4.9 2.7 - - + -
1167A VAL* 3.7 29.8 - - + -
1171A GLN* 3.5 29.6 - - + +
1172A LEU* 4.0 14.8 - - + -
1174A ARG* 5.5 0.7 - - + -
1175A VAL* 3.6 17.0 - - + -
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Residues in contact with ARG1130 (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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1003A ILE* 3.6 28.2 - - + +
1004A HIS 4.8 0.6 - - - +
1005A ASN* 3.0 45.7 - - - +
1123A ALA 5.2 1.4 + - - -
1126A SER* 2.8 34.9 + - - +
1127A ALA* 3.7 24.3 - - - +
1129A LEU* 1.3 77.6 - - - +
1131A LEU* 1.3 52.8 + - - +
1133A THR* 3.0 7.5 + - - -
1134A LEU* 2.7 43.4 + - + +
1175A VAL* 3.7 33.7 - - + +
1259A TRP* 4.9 4.9 - - - -
1260A MET* 3.2 41.1 + - - +
1263A GLU* 4.1 2.3 - - - +
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Residues in contact with LEU1131 (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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995A TRP* 3.6 41.1 - - + -
999A GLY 4.5 0.4 - - - +
1002A ILE* 4.0 22.7 - - + -
1003A ILE* 3.7 16.8 - - + +
1127A ALA 2.9 28.3 + - - +
1128A LEU* 3.7 4.3 - - - +
1130A ARG* 1.3 74.7 - - - +
1132A ARG* 1.3 61.2 + - - +
1134A LEU* 3.2 9.1 + - - +
1136A ALA* 2.9 43.9 + - + +
1140A ALA* 3.9 14.8 - - + +
1141A LEU* 3.8 15.0 - - + -
1144A GLN* 4.1 12.6 - - + +
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Residues in contact with ARG1132 (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 LEU 3.1 14.2 + - - +
1129A LEU* 3.4 20.5 + - - +
1130A ARG 3.1 0.2 - - - -
1131A LEU* 1.3 76.7 - - - +
1133A THR* 1.3 66.0 + - - +
1135A GLY* 3.1 14.4 + - - -
1136A ALA 4.8 5.1 - - - +
1141A LEU* 4.4 12.3 - - + +
1162A ILE* 3.0 30.6 + - + -
1163A MET* 3.9 32.9 + - + +
1165A GLN 2.8 27.7 + - - -
1167A VAL* 3.4 30.1 - - - +
1172A LEU* 4.1 13.7 - - - +
1217A TRP* 5.6 2.6 - - - +
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Residues in contact with THR1133 (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 LEU 2.7 28.4 + - - -
1130A ARG 3.5 4.9 - - - -
1132A ARG* 1.3 77.9 + - - +
1134A LEU* 1.3 56.5 + - - +
1135A GLY 3.1 3.0 + - - -
1172A LEU* 4.9 3.1 - - - +
1175A VAL* 4.2 10.4 - - + +
1217A TRP* 3.2 59.8 + - + +
1257A MET* 3.0 19.9 - - + +
1260A MET* 3.7 21.1 - - + -
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Residues in contact with LEU1134 (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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1002A ILE* 3.5 32.7 - - + +
1003A ILE* 3.7 28.9 - - + -
1130A ARG* 2.7 20.9 + - + +
1131A LEU 3.9 0.7 - - - +
1132A ARG 3.2 0.8 - - - -
1133A THR* 1.3 73.1 - - - +
1135A GLY* 1.3 60.6 + - - +
1136A ALA 3.3 2.3 + - - -
1257A MET* 3.6 40.8 - - + +
1260A MET* 4.0 11.9 - - + -
1261A ARG* 3.5 46.6 + - + +
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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