Contacts of the helix formed by residues 1119 - 1124 (chain A) in PDB entry 1WUF
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 SER1119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1113A ALA* 3.9 0.3 - - - +
1118A ARG* 1.3 80.1 - - - +
1120A LEU* 1.3 63.9 + - - +
1121A ALA* 3.7 3.4 - - - -
1122A LYS* 3.0 35.7 + - - +
1123A MET* 3.1 20.8 + - - +
1343A PRO* 3.4 17.2 + - - -
1344A THR* 2.9 29.7 + - - -
1345A ASN 3.5 13.4 + - - -
1347A GLY 4.4 0.4 - - - -
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Residues in contact with LEU1120 (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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1109A TRP* 4.1 40.8 - - + +
1110A ASP* 4.5 1.3 - - - +
1113A ALA* 3.8 19.3 - - + -
1119A SER* 1.3 74.4 - - - +
1121A ALA* 1.3 62.9 + - - +
1123A MET* 3.5 2.8 + - - -
1124A ILE* 3.1 29.9 + - + +
1270A MET* 4.6 10.3 - - - -
1301A HIS* 4.5 25.6 - - + +
1304A ALA* 3.3 29.6 - - + -
1347A GLY 2.6 26.1 + - - +
1348A ILE* 4.1 8.7 - - + +
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Residues in contact with ALA1121 (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 SER* 3.0 7.2 - - - -
1120A LEU* 1.3 78.7 - - - +
1122A LYS* 1.3 67.6 - - + +
1124A ILE* 3.4 7.8 - - - +
1126A ALA* 3.0 34.5 + - + +
1128A LYS 6.0 0.2 - - - +
1304A ALA* 3.7 24.1 - - + +
1342A VAL* 3.5 32.3 - - + -
1343A PRO* 4.4 1.6 - - + +
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Residues in contact with LYS1122 (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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1118A ARG* 4.3 16.6 + - + -
1119A SER* 3.0 40.0 + - - +
1120A LEU 3.4 0.6 - - - -
1121A ALA* 1.3 76.2 - - + +
1123A MET* 1.3 58.7 + - - +
1125A GLY* 2.8 24.1 + - - -
1126A ALA 4.3 11.6 - - - +
1127A THR* 6.4 0.4 - - - -
1128A LYS 6.0 2.2 - - - -
1129A GLU* 6.4 2.0 - - - -
1342A VAL* 6.6 0.4 - - - -
1343A PRO 5.2 1.3 - - - -
1344A THR* 4.0 26.6 + - - +
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Residues in contact with MET1123 (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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1084A PRO* 5.2 4.5 - - + -
1109A TRP* 4.5 25.6 - - + +
1112A PHE* 4.1 9.2 - - + -
1113A ALA* 3.6 36.8 - - + +
1116A GLU* 2.9 46.7 - - + +
1118A ARG* 3.7 24.3 + - + +
1119A SER 3.1 15.8 + - - +
1120A LEU* 3.6 4.9 - - - +
1121A ALA 3.3 0.2 - - - -
1122A LYS* 1.3 75.3 - - - +
1124A ILE* 1.3 60.5 + - - +
1125A GLY* 2.8 11.4 + - - -
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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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1109A TRP* 3.5 32.5 - - + -
1120A LEU* 3.1 16.7 + - + +
1121A ALA 3.4 13.9 - - - +
1123A MET* 1.3 74.6 - - - +
1125A GLY* 1.3 55.7 + - - +
1126A ALA 4.2 3.6 - - - +
1270A MET* 3.9 26.0 - - + -
1274A LEU* 4.1 11.4 - - + +
1304A ALA* 3.0 36.6 - - + +
1305A LEU* 3.9 9.6 - - - -
1308A ARG* 2.8 43.4 + - + +
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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