Contacts of the helix formed by residues 139 - 149 (chain G) in PDB entry 2W3S
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 TYR 139 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110G PHE* 4.0 7.0 - + - -
132G ASN 3.5 19.5 + - - -
133G LEU* 3.3 10.6 - - - +
134G CYS* 2.7 47.4 + - + -
137G THR* 3.2 12.1 + - - -
138G GLY* 1.3 82.2 - - - +
140G ALA* 1.3 62.5 + - - +
141G PRO* 3.4 3.1 - - - -
142G ILE* 3.0 20.7 + - + +
143G LEU 3.1 9.4 + - - -
669H VAL* 4.7 8.7 - - + -
698H ILE* 5.3 0.5 - - - +
699H PRO* 3.0 37.0 + - + -
700H ALA* 4.0 4.3 - - - -
701H PHE* 3.4 49.9 - + + +
704H ARG* 4.0 20.9 - - + -
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Residues in contact with ALA 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G GLY 2.7 14.1 + - - +
139G TYR* 1.3 71.0 - - - +
141G PRO* 1.4 68.6 - - + +
143G LEU* 2.9 15.9 + - - +
144G ARG* 3.1 25.9 + - - +
665H GLU* 3.4 21.5 - - - +
704H ARG* 4.1 12.1 - - - +
708H PHE* 4.0 18.4 - - + -
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Residues in contact with PRO 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G HIS* 3.3 27.6 - - - +
99G HIS* 3.6 13.9 - - + +
100G GLY* 3.9 4.4 - - - -
102G GLN* 5.7 1.1 - - - +
137G THR* 3.6 39.5 - - - +
139G TYR 3.5 1.1 - - - -
140G ALA* 1.4 95.8 - - + +
142G ILE* 1.3 57.1 + - - +
144G ARG* 3.0 23.6 - - - +
145G ALA* 3.0 26.0 + - - +
662H GLY* 6.2 1.3 - - - -
665H GLU* 3.7 8.5 - - - +
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Residues in contact with ILE 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G MET* 4.2 6.3 - - + -
100G GLY* 3.6 26.5 - - - +
110G PHE* 3.9 47.8 - - + -
114G MET* 4.0 16.8 - - - +
129G LEU* 4.3 3.6 - - + -
134G CYS* 4.6 4.0 - - + -
137G THR* 3.3 23.8 - - - +
139G TYR* 3.0 21.0 + - + +
141G PRO* 1.3 74.3 - - - +
143G LEU* 1.3 58.9 + - - +
145G ALA* 3.2 7.9 + - - +
146G ALA* 2.9 25.8 + - - +
701H PHE* 4.1 11.0 - - + -
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Residues in contact with LEU 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G TYR* 4.9 15.5 - - + -
126G ASP* 4.8 1.6 - - - +
139G TYR 3.1 6.2 + - - +
140G ALA* 2.9 12.4 + - - +
142G ILE* 1.3 74.1 - - - +
144G ARG* 1.3 68.8 + - + +
146G ALA* 2.9 16.8 + - - +
147G GLU* 3.0 46.3 + - + +
701H PHE* 4.1 19.5 - - + -
704H ARG* 3.2 39.5 - - - +
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Residues in contact with ARG 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G HIS* 3.9 27.0 + - + +
140G ALA* 3.1 14.2 + - - +
141G PRO* 3.0 40.2 - - - +
143G LEU* 1.3 76.4 - - + +
145G ALA* 1.3 51.6 + - - +
147G GLU* 3.2 14.8 + - - +
148G ALA* 2.7 37.7 + - - +
661H ILE* 6.0 0.8 - - - +
665H GLU* 3.1 31.5 + - - -
708H PHE* 4.6 11.3 + - - +
710H VAL* 6.0 0.2 - - - +
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Residues in contact with ALA 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G VAL* 5.8 1.1 - - - +
94G ALA* 3.3 33.7 - - + +
95G MET* 3.7 28.9 - - + +
98G HIS* 4.2 5.8 - - + +
100G GLY* 5.6 0.2 - - - -
114G MET* 5.3 1.3 - - - -
141G PRO 3.0 14.7 + - - +
142G ILE 3.4 9.0 - - - +
143G LEU 3.1 0.4 - - - -
144G ARG* 1.3 72.7 - - - +
146G ALA* 1.3 67.8 + - - +
148G ALA* 4.2 2.7 - - - -
149G ALA* 3.2 20.4 + - - +
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Residues in contact with ALA 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G VAL* 6.1 3.4 - - - -
114G MET* 5.0 16.4 - - + -
118G HIS* 6.0 0.2 - - - -
125G TYR* 3.4 50.2 + - + -
129G LEU* 5.3 4.0 - - + -
142G ILE 2.9 12.3 + - - +
143G LEU* 2.9 10.5 + - - +
145G ALA* 1.3 76.0 - - - +
147G GLU* 1.3 63.5 + - - +
149G ALA* 4.0 2.1 - - - +
150G ALA* 3.3 14.6 + - - +
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Residues in contact with GLU 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G TYR* 4.3 16.4 - - + -
143G LEU* 3.0 40.6 + - + +
144G ARG* 3.5 13.6 - - - +
146G ALA* 1.3 76.5 - - - +
148G ALA* 1.3 67.3 + - - +
150G ALA* 2.9 23.0 + - - +
151G GLY 3.9 2.1 + - - -
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Residues in contact with ALA 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G ALA* 4.1 7.4 - - + -
98G HIS* 3.7 29.2 - - + +
144G ARG 2.7 21.1 + - - +
145G ALA 3.4 5.6 + - - +
147G GLU* 1.3 74.6 - - - +
149G ALA* 1.3 58.9 + - - +
151G GLY* 4.0 9.5 + - - +
152G GLU* 5.0 1.9 - - - +
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Residues in contact with ALA 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G PRO* 3.1 40.4 - - + +
91G VAL* 4.0 10.1 - - + +
94G ALA* 3.6 10.3 - - + -
118G HIS* 3.1 20.8 + - + +
145G ALA 3.2 6.6 + - - +
146G ALA 4.0 1.8 - - - +
147G GLU 3.2 0.4 - - - -
148G ALA* 1.3 77.1 - - - +
150G ALA* 1.3 65.7 + - - +
151G GLY 3.3 1.1 - - - -
152G GLU* 3.2 16.1 - - - +
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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