Contacts of the strand formed by residues 1134 - 1138 (chain A) in PDB entry 2NZ6
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 ALA1134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1132A VAL* 3.2 7.3 - - - +
1133A TYR* 1.3 81.0 - - + +
1135A ILE* 1.3 62.2 + - - +
1136A ILE* 4.9 0.9 - - + -
1196A ARG* 3.3 6.3 - - + +
1198A PHE* 4.3 11.9 - - + -
1226A MET* 4.1 28.9 - - + -
1234A PRO 4.8 1.8 + - - -
1235A ILE* 3.8 20.4 - - + -
1236A LEU 3.1 23.4 + - - -
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Residues in contact with ILE1135 (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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1123A PHE* 4.5 6.7 - - + -
1124A TRP* 4.5 8.1 - - + -
1127A VAL* 4.2 15.9 - - + -
1132A VAL* 4.1 12.3 - - + -
1134A ALA* 1.3 75.7 - - - +
1136A ILE* 1.3 67.6 + - - +
1137A MET 4.1 0.2 - - - -
1152A TYR* 3.5 27.4 - - + +
1182A PHE* 6.1 0.2 - - + -
1195A LEU* 3.8 33.2 - - + -
1196A ARG 2.9 8.0 + - - +
1197A GLN* 3.3 12.5 - - + +
1198A PHE* 2.8 31.9 + - - +
1236A LEU* 3.3 16.2 - - + +
1238A HIS* 3.8 18.4 - - + +
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Residues in contact with ILE1136 (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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1134A ALA* 4.9 0.9 - - + -
1135A ILE* 1.3 84.1 - - - +
1137A MET* 1.3 60.1 + - - +
1138A LEU* 3.9 13.5 - - + -
1198A PHE* 3.4 18.6 - - + -
1218A PHE* 3.7 28.0 - - + -
1222A VAL* 3.5 29.8 - - + -
1235A ILE* 3.8 23.1 - - + -
1236A LEU 2.6 12.6 + - - +
1237A VAL* 3.9 15.0 - - + +
1238A HIS* 2.8 31.2 + - - +
1249A PHE* 4.0 17.9 - - + -
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Residues in contact with MET1137 (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 ILE 4.1 0.4 - - - -
1136A ILE* 1.3 71.9 - - - +
1138A LEU* 1.3 63.6 + - - +
1139A THR* 3.3 27.1 - - + -
1151A GLU* 5.9 1.8 - - - +
1152A TYR* 3.8 8.5 - - + +
1153A TRP* 3.6 34.5 - - + -
1197A GLN* 4.1 7.9 - - + +
1198A PHE 2.9 11.6 + - - +
1199A HIS* 3.3 30.4 - - + +
1200A PHE 2.9 27.4 + - - -
1238A HIS* 3.3 37.9 - - + +
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Residues in contact with LEU1138 (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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1136A ILE* 3.9 8.7 - - + -
1137A MET* 1.3 73.9 - - - +
1139A THR* 1.3 64.9 + - - +
1200A PHE* 3.8 19.7 - - + -
1203A TRP* 3.6 32.3 - - + -
1218A PHE* 3.9 18.2 - - + -
1237A VAL* 3.8 14.8 - - + -
1238A HIS 3.1 10.7 + - - +
1239A SER* 3.6 20.3 - - - -
1240A SER 4.8 0.3 + - - -
1245A ARG* 3.3 50.6 + - + +
1246A THR* 3.7 10.5 - - - +
1249A PHE* 3.9 7.2 - - + -
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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