Contacts of the helix formed by residues 112 - 122 (chain K) in PDB entry 1UW9
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 SER 112 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E ASN* 4.8 0.2 + - - -
244E ALA* 3.8 1.9 - - - -
245E GLY* 3.4 31.7 + - - -
109K GLU* 3.3 24.6 + - - -
110K GLU 3.3 1.2 - - - -
111K GLY* 1.3 76.1 - - - +
113K VAL* 1.3 63.5 + - - +
114K THR* 3.7 3.1 - - - +
115K ASN* 3.0 32.1 + - - +
116K MET 3.2 9.7 + - - -
144K TYR* 3.5 8.7 + - - -
148K PHE* 3.5 5.4 - - - -
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Residues in contact with VAL 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E GLY* 5.1 1.0 + - - -
111K GLY 3.9 0.8 + - - -
112K SER* 1.3 71.6 - - - +
114K THR* 1.3 63.5 + - - +
116K MET* 3.1 9.7 + - + +
117K PHE* 2.9 28.9 + - + +
148K PHE* 3.6 22.7 - - + -
274K PHE* 3.6 42.2 - - + -
278K THR* 5.4 4.6 + - - +
317K ALA* 3.4 35.0 - - + +
320K MET* 3.7 9.9 - - + -
321K SER* 3.7 15.5 - - - +
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Residues in contact with THR 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E ASN* 5.0 0.2 - - - +
243E THR* 3.4 33.2 - - + -
244E ALA 3.6 16.9 + - - +
245E GLY* 4.7 2.4 - - - -
271E THR* 2.8 37.0 + - - +
272E GLY* 3.7 2.7 - - - +
112K SER* 3.7 2.9 - - - +
113K VAL* 1.3 78.5 - - - +
115K ASN* 1.3 53.4 + - - +
117K PHE* 3.4 4.4 + - - +
118K THR* 2.7 35.6 + - - +
274K PHE* 3.5 14.4 - - - +
275K THR* 3.1 14.6 + - - -
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Residues in contact with ASN 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E ASN* 2.9 33.5 + - - +
207E ASN* 3.1 26.4 + - - +
209E GLN* 3.7 2.6 - - - +
107K LEU 3.7 5.4 - - - +
108K PHE* 3.4 12.1 - - - +
109K GLU* 2.9 32.6 + - + +
112K SER* 3.0 27.7 + - - +
114K THR* 1.3 75.0 - - - +
116K MET* 1.3 62.8 + - - +
118K THR* 3.2 4.1 + - - -
119K SER* 3.2 22.3 + - - -
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Residues in contact with MET 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K ILE* 4.9 3.6 - - + -
108K PHE* 3.8 22.4 - - + -
112K SER 3.2 11.3 + - - +
113K VAL* 3.1 14.4 + - + +
115K ASN* 1.3 78.1 + - - +
117K PHE* 1.3 82.7 + - + +
119K SER* 3.5 1.0 + - - -
120K ILE* 3.1 42.9 + - + +
138K LEU* 3.7 22.4 - - + -
140K ILE* 3.7 24.2 - - + -
144K TYR* 4.0 13.7 - - + +
316K LYS* 6.5 0.2 - - + -
317K ALA* 4.9 2.9 - - + +
320K MET* 4.0 27.8 - - + -
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Residues in contact with PHE 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E THR* 4.3 11.4 - - + -
297E MET* 4.4 14.6 - - + -
113K VAL* 2.9 20.4 + - + +
114K THR* 3.8 4.0 - - - +
116K MET* 1.3 91.5 - - + +
118K THR* 1.3 61.7 + - - +
120K ILE* 5.0 2.2 - - + -
121K VAL* 2.8 54.1 + - + +
122K GLY 3.3 1.2 + - - -
135K LEU* 5.8 1.6 - - + -
138K LEU* 4.9 2.7 - - + -
270K LEU* 5.9 0.2 - - + -
274K PHE* 3.9 22.4 - + + -
309K ILE* 4.2 11.0 - - + -
313K VAL* 4.1 18.8 - - + -
314K LEU* 3.9 26.9 - - + -
317K ALA* 3.7 32.1 - - + -
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Residues in contact with THR 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E GLU* 3.3 39.2 - - + +
205E ASN* 3.8 4.7 - - - +
207E ASN* 5.6 0.4 - - - -
243E THR* 4.8 0.3 - - - +
268E ASP* 3.3 23.8 + - - +
271E THR* 2.8 25.6 + - - -
296E ALA* 4.1 6.3 - - + -
114K THR* 2.7 24.8 + - - +
115K ASN* 3.2 10.0 + - - -
117K PHE* 1.3 75.7 - - - +
119K SER* 1.3 58.8 + - - +
122K GLY* 3.1 24.6 - - - -
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Residues in contact with SER 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E LEU* 3.9 9.4 - - - +
204E GLU* 5.8 0.2 - - - -
205E ASN* 2.8 34.3 + - - +
60K GLU 4.8 0.7 - - - +
61K SER* 3.1 35.2 + - - -
103K TYR* 5.5 0.9 - - - -
107K LEU* 4.7 5.3 + - - +
108K PHE* 4.3 15.7 - - - -
115K ASN* 3.2 12.0 + - - -
116K MET 3.9 5.8 - - - -
118K THR* 1.3 80.9 - - - +
120K ILE* 1.3 65.4 + - - +
121K VAL 3.4 0.2 + - - -
122K GLY* 3.7 3.8 + - - -
123K ASN 5.1 1.0 + - - -
124K VAL* 5.5 0.3 - - - +
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Residues in contact with ILE 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K ILE* 3.8 29.2 - - + -
38K ALA* 4.2 2.7 - - + -
40K PHE* 3.5 34.9 - - + -
61K SER* 4.2 6.6 - - - -
103K TYR* 3.9 22.2 - - + +
108K PHE* 4.1 11.9 - - + -
116K MET* 3.1 30.6 + - + +
117K PHE* 5.0 1.6 - - + -
119K SER* 1.3 76.6 - - - +
121K VAL* 1.3 61.6 + - + +
124K VAL* 3.7 10.8 - - - +
135K LEU* 4.1 21.1 - - + -
138K LEU* 3.8 18.4 - - + -
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Residues in contact with VAL 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E MET* 3.4 25.5 - - + -
300E VAL* 3.8 10.3 - - + +
40K PHE* 5.0 0.2 - - + -
117K PHE* 2.8 43.8 + - + +
120K ILE* 1.3 78.3 - - + +
122K GLY* 1.3 62.8 + - - +
123K ASN 3.7 1.6 - - - -
124K VAL 4.9 0.9 - - - -
125K PHE* 3.5 35.0 - - + +
135K LEU* 3.7 28.9 - - + -
309K ILE* 3.9 21.3 - - + -
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Residues in contact with GLY 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E GLU* 5.3 0.2 - - - -
295E ARG 4.6 0.2 - - - +
296E ALA* 3.3 11.2 - - - -
297E MET* 2.7 29.7 + - - -
298E HIS* 4.6 4.9 + - - -
299E ALA* 5.5 1.9 + - - +
117K PHE 3.3 1.9 + - - -
118K THR* 3.1 26.1 + - - -
119K SER 3.7 1.6 + - - -
120K ILE 3.7 1.8 - - - -
121K VAL* 1.3 76.8 - - - +
123K ASN* 1.3 69.7 + - - +
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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