Contacts of the helix formed by residues 140 - 149 (chain Y) in PDB entry 2W4T
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 ASP 140 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Y LYS* 3.3 16.6 - - - +
103Y LYS* 3.8 25.1 - - + +
133Y PRO* 3.5 18.4 + - + +
135Y GLU* 4.8 4.5 - - - +
138Y LYS 3.5 5.8 + - - +
139Y PHE* 1.3 68.7 - - - +
141Y TYR* 1.3 58.3 + - - +
142Y VAL* 3.0 10.8 + - - +
143Y LYS* 2.6 44.4 + - + +
144Y PHE* 3.3 21.5 + - - +
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Residues in contact with TYR 141 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811C ILE* 4.7 17.5 - - + +
814C ASN* 5.1 5.9 + - - -
89Y ILE* 2.8 40.8 + - - +
90Y ARG* 3.2 15.9 - - + -
93Y PHE* 2.7 81.1 - + + -
102Y LYS 4.8 0.4 + - - -
103Y LYS* 4.7 1.8 - - - +
139Y PHE* 3.0 11.0 + + - -
140Y ASP* 1.3 69.8 - - - +
142Y VAL* 1.3 56.6 + - - +
144Y PHE* 4.1 24.0 - + - -
145Y THR* 2.3 55.5 + - - -
148Y ILE* 6.0 0.5 - - - +
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Residues in contact with VAL 142 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90Y ARG* 4.6 24.9 - - + -
93Y PHE* 5.9 1.6 - - + -
102Y LYS* 3.9 41.5 - - + +
140Y ASP* 3.0 10.2 + - - +
141Y TYR* 1.3 78.5 - - + +
143Y LYS* 1.3 61.3 + - - +
144Y PHE 3.0 0.7 - - - -
145Y THR* 2.6 29.0 + - - -
146Y ALA* 2.9 12.0 + - + +
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Residues in contact with LYS 143 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133Y PRO* 4.5 21.3 - - + -
140Y ASP* 2.6 26.5 + - + +
142Y VAL* 1.3 75.1 - - - +
144Y PHE* 1.3 51.2 + - - +
146Y ALA* 3.5 7.6 + - + +
147Y MET* 2.6 60.0 + - + +
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Residues in contact with PHE 144 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814C ASN* 6.3 0.4 - - - -
815C ILE* 4.2 15.0 - - + -
818C TRP* 3.5 30.5 - + - -
128Y THR* 4.2 11.7 - - - -
131Y GLU* 4.9 1.3 - - + -
132Y ALA* 4.0 11.7 - - + -
133Y PRO* 3.5 16.4 - - + +
139Y PHE* 3.3 34.3 - + + -
140Y ASP 3.3 17.0 + - - +
141Y TYR* 4.1 18.2 - + - -
142Y VAL 3.0 0.8 - - - -
143Y LYS* 1.3 76.7 - - - +
145Y THR* 1.3 56.3 + - - +
146Y ALA 3.2 0.2 - - - -
147Y MET* 3.9 9.2 - - + -
148Y ILE* 2.2 65.4 + - + +
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Residues in contact with THR 145 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Y GLU* 3.6 11.2 - - + +
89Y ILE* 2.7 44.0 - - + -
90Y ARG* 4.1 4.7 - - + +
141Y TYR* 2.3 51.3 + - - -
142Y VAL* 2.6 14.6 + - - -
144Y PHE* 1.3 71.7 - - - +
146Y ALA* 1.3 63.6 + - - -
148Y ILE* 3.0 22.2 - - + +
149Y LYS* 3.0 9.9 + - - +
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Residues in contact with ALA 146 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Y GLU* 6.0 2.0 - - - -
142Y VAL* 2.9 9.4 + - + +
143Y LYS* 3.6 11.9 - - + +
145Y THR* 1.3 75.1 - - - +
147Y MET* 1.3 59.4 + - + +
149Y LYS* 2.5 39.3 + - - -
150Y GLY 3.5 16.5 + - - +
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Residues in contact with MET 147 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818C TRP* 4.1 18.3 + - + -
822C ARG* 4.2 4.9 + - - +
131Y GLU* 5.6 13.0 - - + +
133Y PRO* 5.1 7.2 - - + -
143Y LYS* 2.6 50.9 - - + +
144Y PHE* 3.9 12.8 - - + +
145Y THR 3.5 0.2 - - - -
146Y ALA* 1.3 76.1 - - - +
148Y ILE* 1.3 62.1 + - + +
149Y LYS 3.4 5.4 + - - +
150Y GLY* 5.1 2.2 - - - +
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Residues in contact with ILE 148 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814C ASN* 4.3 26.2 - - + +
815C ILE* 5.5 0.7 - - + -
818C TRP* 3.7 41.6 - - + +
89Y ILE* 5.4 10.1 - - + -
141Y TYR* 6.0 0.7 - - - +
144Y PHE* 2.2 69.8 - - + +
145Y THR* 3.0 25.4 - - + +
146Y ALA 3.1 0.4 - - - -
147Y MET* 1.3 74.9 - - - +
149Y LYS* 1.3 65.0 + - + +
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Residues in contact with LYS 149 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Y ASP 3.6 17.6 + - - +
85Y SER* 3.6 3.5 - - - +
86Y GLU* 2.3 73.9 + - + +
89Y ILE* 4.3 2.0 - - + -
145Y THR 3.0 17.0 + - - +
146Y ALA* 2.5 18.7 + - - +
147Y MET 3.8 4.3 - - - +
148Y ILE* 1.3 82.0 - - + +
150Y GLY* 1.3 76.1 + - - +
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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