Contacts of the helix formed by residues 112 - 122 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H GLU* 3.3 25.3 + - - -
110H GLU 3.2 1.2 - - - -
111H GLY* 1.3 77.7 - - - +
113H VAL* 1.3 62.7 + - - +
114H THR* 3.7 2.8 - - - -
115H ASN* 3.0 32.9 + - - +
116H MET* 3.2 9.0 + - - +
144H TYR* 3.4 9.7 + - - -
148H PHE* 3.4 5.1 - - - -
207R ASN* 4.8 0.2 + - - -
244R ALA* 3.8 2.3 - - - -
245R GLY* 3.3 31.3 + - - -
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Residues in contact with VAL 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H GLY 3.9 0.8 + - - -
112H SER* 1.3 73.5 - - - +
114H THR* 1.3 63.2 + - - +
116H MET* 3.1 9.1 + - + +
117H PHE* 2.9 29.2 + - + +
148H PHE* 3.6 21.9 - - + -
274H PHE* 3.5 42.8 - - + -
278H THR* 5.3 4.3 + - - +
317H ALA* 3.5 33.7 - - + +
320H MET* 3.7 15.3 - - + -
321H SER* 3.7 11.7 - - - +
245R GLY* 5.1 0.6 - - - -
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Residues in contact with THR 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H SER* 3.7 3.1 - - - +
113H VAL* 1.3 79.7 - - - +
115H ASN* 1.3 53.3 + - - +
117H PHE* 3.6 2.3 + - - +
118H THR* 2.6 35.7 + - - -
274H PHE* 3.5 13.2 - - - +
275H THR* 3.1 15.9 + - - -
243R THR* 3.4 32.3 - - + -
244R ALA 3.6 15.8 + - - +
245R GLY* 4.7 1.8 - - - -
271R THR* 2.9 39.6 + - - +
272R GLY* 3.7 4.0 - - - +
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Residues in contact with ASN 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H LEU 3.7 1.9 - - - +
108H PHE* 3.4 11.8 - - - +
109H GLU* 2.9 32.6 + - + +
112H SER* 3.0 27.5 + - - +
114H THR* 1.3 73.9 - - - +
116H MET* 1.3 66.1 + - - +
118H THR* 3.2 3.9 + - - -
119H SER* 3.2 22.1 + - - -
205R ASN* 2.9 32.7 + - - +
207R ASN* 3.1 27.1 + - - +
209R GLN* 3.7 5.9 + - - +
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Residues in contact with MET 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H ILE* 5.0 4.3 - - - -
108H PHE* 3.8 22.4 - - + -
112H SER 3.2 9.3 + - - +
113H VAL* 3.1 13.3 + - + +
115H ASN* 1.3 79.8 + - - +
117H PHE* 1.3 82.7 + - + +
119H SER* 3.4 1.2 + - - -
120H ILE* 3.0 42.1 + - + +
138H LEU* 3.7 23.1 - - + -
140H ILE* 3.6 24.2 - - + -
144H TYR* 4.0 13.2 + - + +
316H LYS* 6.5 0.4 - - + -
317H ALA* 4.9 3.4 - - + -
320H MET* 3.8 28.5 - - + -
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Residues in contact with PHE 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H VAL* 2.9 21.0 + - + +
114H THR* 3.9 4.9 - - - +
116H MET* 1.3 93.5 - - + +
118H THR* 1.3 57.4 + - - +
120H ILE* 5.0 1.6 - - + -
121H VAL* 2.8 54.1 + - + +
122H GLY* 3.3 1.6 + - - -
135H LEU* 5.8 1.6 - - + -
138H LEU* 4.8 2.9 - - + -
270H LEU* 6.0 0.4 - - + -
274H PHE* 3.9 22.7 - + + -
309H ILE* 4.1 11.9 - - + -
313H VAL* 4.2 19.5 - - + -
314H LEU* 3.9 25.1 - - + -
317H ALA* 3.7 32.1 - - + -
271R THR* 4.3 11.2 - - + -
297R MET* 4.4 15.0 - - + -
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Residues in contact with THR 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H THR* 2.6 25.6 + - - +
115H ASN* 3.2 9.7 + - - -
117H PHE* 1.3 76.8 - - - +
119H SER* 1.3 58.1 + - - +
122H GLY* 3.0 24.7 - - - -
204R GLU* 3.3 51.3 - - + +
205R ASN* 3.8 4.7 - - - +
207R ASN* 5.5 0.7 - - - -
243R THR* 4.8 0.7 - - - +
268R ASP* 3.3 10.8 + - - +
271R THR* 2.8 24.7 + - - -
296R ALA* 4.1 6.7 - - + -
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Residues in contact with SER 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H GLU 4.8 0.5 - - - +
61H SER* 3.1 35.8 - - - -
103H TYR* 5.5 1.1 - - - -
107H LEU* 4.7 5.5 + - - -
108H PHE* 4.4 14.8 - - - -
115H ASN* 3.2 11.3 + - - -
116H MET 3.9 5.2 - - - -
118H THR* 1.3 80.5 - - - +
120H ILE* 1.3 65.6 + - - +
121H VAL 3.4 0.2 + - - -
122H GLY* 3.7 3.3 + - - -
123H ASN 5.1 1.2 + - - -
124H VAL* 5.4 0.3 - - - +
177R LYS* 6.3 0.2 - - - +
178R LEU* 3.9 10.3 - - - +
205R ASN* 2.8 34.9 + - - +
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Residues in contact with ILE 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H ILE* 3.8 29.4 - - + -
38H ALA* 4.2 2.5 - - + -
40H PHE* 3.5 33.6 - - + -
61H SER* 4.2 6.4 - - - -
103H TYR* 3.9 23.3 - - + +
108H PHE* 4.1 11.4 - - + -
116H MET* 3.0 30.6 + - + +
117H PHE* 4.6 1.3 - - + +
119H SER* 1.3 76.8 - - - +
121H VAL* 1.3 59.9 + - + +
124H VAL* 3.7 10.7 - - - +
135H LEU* 4.1 12.3 - - + -
138H LEU* 3.8 27.4 - - + -
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Residues in contact with VAL 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H PHE* 2.8 49.0 + - + +
120H ILE* 1.3 80.6 - - + +
122H GLY* 1.3 65.1 + - - +
123H ASN 3.7 1.3 - - - -
124H VAL 4.9 0.7 - - - -
125H PHE* 3.5 31.3 - - + +
135H LEU* 3.7 29.6 - - + -
309H ILE* 3.9 17.3 - - + -
297R MET* 3.4 25.8 - - + -
300R VAL* 3.7 10.8 - - + +
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Residues in contact with GLY 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H PHE 3.3 1.5 + - - -
118H THR* 3.0 26.1 + - - -
119H SER 3.7 1.6 + - - -
120H ILE 3.7 1.6 - - - -
121H VAL* 1.3 77.8 - - - +
123H ASN* 1.3 68.6 + - - +
124H VAL* 5.2 0.2 - - - +
204R GLU* 5.3 0.4 - - - -
295R ARG 4.6 0.5 - - - +
296R ALA* 3.4 11.5 - - - -
297R MET* 2.7 28.8 + - - -
298R HIS* 4.6 4.7 + - - -
299R ALA* 5.5 1.9 + - - +
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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