Contacts of the helix formed by residues 1122 - 1132 (chain A) in PDB entry 6CNB
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 GLY1122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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878A LYS* 6.0 2.0 - - - -
1120A THR* 3.5 5.3 - - - +
1121A LEU* 1.3 82.3 - - - +
1123A VAL* 1.3 62.9 + - - -
1124A PRO* 3.2 11.7 - - - -
1125A ARG* 2.9 22.6 + - - +
1126A ILE* 3.9 2.4 + - - +
1342A THR* 4.6 1.7 + - - -
1346A HIS* 3.4 13.5 - - - -
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Residues in contact with VAL1123 (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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878A LYS* 3.8 31.3 - - + +
881A GLU* 4.7 10.5 - - - +
882A THR* 5.1 4.7 - - - +
885A MET* 3.6 35.7 - - + -
1100A PRO 5.0 10.5 - - - +
1122A GLY* 1.3 71.4 - - - -
1124A PRO* 1.3 70.4 - - + +
1126A ILE* 2.8 32.1 + - + +
1127A LYS* 3.0 9.5 + - + +
1346A HIS* 4.1 7.5 + - + -
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Residues in contact with PRO1124 (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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878A LYS* 5.2 8.1 - - - +
1120A THR* 5.8 5.4 - - - -
1122A GLY* 3.2 10.8 - - - +
1123A VAL* 1.3 98.9 - - + +
1125A ARG* 1.3 61.3 + - - +
1127A LYS* 3.1 37.3 - - + +
1128A GLU* 3.1 17.4 + - - +
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Residues in contact with ARG1125 (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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1119A VAL* 5.7 3.1 - - - +
1120A THR* 3.1 40.8 + - - +
1121A LEU* 4.6 2.7 - - - +
1122A GLY 2.9 15.9 + - - +
1124A PRO* 1.3 77.3 - - - +
1126A ILE* 1.3 67.0 + - - +
1128A GLU* 2.9 10.2 + - - +
1129A ILE* 2.9 36.2 + - + +
1136A ILE* 3.3 33.4 - - - +
1137A SER 4.4 4.8 + - - -
1138A THR* 4.9 4.0 + - - +
1317A ASN* 3.1 31.2 - - - +
1318A HIS 3.9 2.8 - - - +
1338A GLU* 2.3 37.1 + - - +
1342A THR* 4.7 15.7 - - - +
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Residues in contact with ILE1126 (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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885A MET* 3.6 30.7 - - + -
1097A ILE* 5.3 5.2 - - + -
1122A GLY 5.0 1.3 - - - +
1123A VAL* 2.8 24.9 + - + +
1125A ARG* 1.3 73.2 - - - +
1127A LYS* 1.3 64.5 + - - +
1129A ILE* 4.4 6.1 - - - +
1130A ILE* 2.9 45.6 + - + +
1339A ILE* 4.4 13.0 - - + -
1342A THR* 4.1 25.1 - - + +
1343A MET* 4.4 26.5 - - + -
1346A HIS* 6.0 4.5 - - + -
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Residues in contact with LYS1127 (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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881A GLU* 2.5 55.6 + - + +
884A TYR* 4.8 6.1 - - - -
885A MET* 5.1 9.2 - - - -
888A ARG* 3.8 29.8 + - - +
1123A VAL* 3.0 9.9 + - + +
1124A PRO* 3.1 34.8 - - + +
1126A ILE* 1.3 77.4 - - - +
1128A GLU* 1.3 51.8 + - + +
1130A ILE* 5.0 1.1 - - - -
1131A ASN* 2.6 42.3 + - - +
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Residues in contact with GLU1128 (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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1120A THR* 5.3 1.0 + - - -
1124A PRO* 3.1 13.9 + - - +
1125A ARG* 2.9 12.2 + - - +
1127A LYS* 1.3 78.6 - - + +
1129A ILE* 1.3 58.4 + - - +
1131A ASN* 4.1 4.3 - - + +
1132A ALA* 2.6 30.8 + - - -
1133A SER* 3.8 13.5 + - - +
1135A VAL 5.1 2.5 - - - +
1136A ILE* 3.1 43.1 - - + +
1137A SER* 4.0 16.2 + - - -
52X A 5.1 9.3 + - - +
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Residues in contact with ILE1129 (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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1125A ARG* 2.9 59.9 + - + +
1126A ILE 4.1 1.3 - - - +
1128A GLU* 1.3 74.3 - - - +
1130A ILE* 1.3 70.6 + - + +
1132A ALA* 3.2 15.5 + - - +
1136A ILE* 5.2 2.5 - - + -
1318A HIS* 5.7 3.1 - - - +
1319A VAL* 4.6 11.4 - - + +
1335A ILE* 3.6 39.0 - - + +
1338A GLU* 3.3 28.0 - - + +
1339A ILE* 3.6 23.6 - - + -
1342A THR* 5.2 2.9 - - + -
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Residues in contact with ILE1130 (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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885A MET* 4.9 6.3 - - + -
888A ARG* 5.2 5.4 - - - +
889A LEU* 3.8 32.1 - - + -
1097A ILE* 5.2 2.7 - - + -
1126A ILE* 2.9 37.8 + - + +
1127A LYS* 4.4 2.0 - - - +
1129A ILE* 1.3 79.4 - - + +
1131A ASN* 1.3 65.9 + - + +
1132A ALA* 3.0 4.2 + - - +
1335A ILE* 5.4 0.4 - - + -
1339A ILE* 5.0 4.9 - - + -
1358A LEU* 4.0 22.9 - - + -
1362A MET* 3.3 22.5 - - + +
1370A GLY 3.8 6.1 + - - +
1371A ILE* 3.4 37.7 - - + -
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Residues in contact with ASN1131 (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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888A ARG* 4.0 23.8 - - - +
1127A LYS* 2.6 28.3 + - - +
1128A GLU* 4.1 4.2 - - - +
1130A ILE* 1.3 76.9 - - - +
1132A ALA* 1.3 69.1 + - - +
1133A SER* 4.9 10.6 + - - +
1370A GLY 3.6 15.1 + - - +
1371A ILE* 4.9 1.6 - - - -
1372A THR* 3.6 29.0 + - - +
52X A 5.4 12.3 + - - -
53X T 5.4 2.9 + - - -
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Residues in contact with ALA1132 (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 GLU 2.6 21.4 + - - -
1129A ILE* 3.4 13.5 - - - +
1130A ILE 3.1 5.4 - - - +
1131A ASN* 1.3 76.6 - - - +
1133A SER* 1.3 60.7 + - - +
1134A LYS* 5.7 1.4 + - - +
1319A VAL* 5.9 5.4 - - + -
1320A LEU* 5.1 13.0 - - + +
1362A MET* 4.8 4.0 - - - -
1368A VAL* 4.5 24.7 - - + +
1369A LEU* 5.1 3.5 - - - -
1370A GLY 5.1 6.5 - - - +
53X T 5.7 0.2 + - - -
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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