Contacts of the helix formed by residues 135 - 143 (chain G) in PDB entry 1W4R
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 ALA 135 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100G GLN 4.8 3.2 + - - -
102G PHE 5.2 1.9 + - - +
103G PRO* 4.6 14.1 - - + +
105G ILE* 4.2 18.3 - - + +
106G VAL* 3.9 10.7 - - + +
133G PHE 3.4 0.2 + - - -
134G GLY* 1.3 71.9 - - - -
136G ILE* 1.3 64.4 + - - +
137G LEU 3.2 2.9 - - - -
138G ASN* 3.0 38.2 + - - +
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Residues in contact with ILE 136 (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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23G VAL* 5.2 1.8 - - + +
25G LEU* 4.2 12.2 - - + +
99G GLY 3.9 17.7 - - - +
100G GLN* 4.3 6.4 - - - +
105G ILE* 4.2 9.3 - - + +
121G VAL* 4.1 5.8 - - + -
123G ALA* 3.5 31.2 - - + -
124G LEU 3.6 16.4 - - - +
125G ASP* 4.1 7.2 - - - +
133G PHE 3.1 19.7 - - - +
134G GLY 3.3 1.2 - - - -
135G ALA* 1.3 77.9 - - - +
137G LEU* 1.3 76.2 + - + +
139G LEU* 3.0 50.5 + - + +
140G VAL* 4.3 1.9 + - - +
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Residues in contact with LEU 137 (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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137F LEU* 3.3 55.2 - - + +
140F VAL* 4.0 22.4 - - + -
141F PRO* 3.7 22.7 - - + -
25G LEU* 4.1 16.4 - - + -
125G ASP* 4.2 7.4 - - + +
132G PRO* 3.8 22.7 - - + -
134G GLY 5.1 0.6 + - - -
135G ALA 3.1 1.0 + - - -
136G ILE* 1.3 92.8 - - + +
138G ASN* 1.3 57.5 + - - +
139G LEU 3.0 0.4 - - - -
140G VAL* 2.9 27.1 + - + +
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Residues in contact with ASN 138 (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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130F ARG 5.2 0.5 - - - +
132F PRO* 3.4 28.2 - - + +
106G VAL* 3.6 18.2 - - + +
135G ALA* 3.0 31.9 + - - +
137G LEU* 1.3 78.5 - - - +
139G LEU* 1.3 58.0 + - - +
141G PRO* 3.4 13.1 - - - +
142G LEU* 3.6 17.0 - - - +
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Residues in contact with LEU 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ILE* 4.7 6.9 - - + +
23G VAL* 4.0 25.4 - - + -
105G ILE* 3.8 15.5 - - + +
106G VAL* 3.9 24.5 - - + -
109G CYS* 3.8 25.8 - - + -
121G VAL* 4.1 16.4 - - + -
135G ALA 4.2 0.2 + - - -
136G ILE* 3.0 38.4 + - + +
138G ASN* 1.3 77.0 - - - +
140G VAL* 1.3 65.8 + - + +
141G PRO 3.4 0.2 - - - -
142G LEU* 2.9 22.8 + - + +
143G ALA* 3.0 14.7 + - - +
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Residues in contact with VAL 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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25F LEU* 4.0 11.2 - - + -
125F ASP* 3.1 15.8 - - + +
137F LEU* 3.9 24.0 - - + -
140F VAL* 5.5 2.5 - - + -
148F LYS* 3.0 20.1 + - + +
23G VAL* 5.3 4.3 - - + -
25G LEU* 4.5 7.0 - - + -
136G ILE 4.8 1.6 - - - +
137G LEU* 2.9 36.9 + - + +
139G LEU* 1.3 76.7 - - + +
141G PRO* 1.3 65.5 - - + +
143G ALA* 3.1 9.9 + - - +
146G VAL* 4.2 32.5 - - + -
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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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125F ASP* 3.2 24.0 - - - +
126F GLY* 3.8 14.7 - - - -
130F ARG* 3.5 30.2 - - - +
131F LYS 3.9 0.4 - - - -
132F PRO* 3.7 27.1 - - + -
137F LEU* 3.8 4.3 - - + -
148F LYS* 4.0 1.7 + - - -
162F TYR* 3.3 23.4 - - - -
137G LEU 3.5 6.7 - - - +
138G ASN 3.4 13.0 - - - +
140G VAL* 1.3 95.2 - - + +
142G LEU* 1.3 56.0 + - - +
143G ALA 3.4 0.2 - - - -
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Residues in contact with LEU 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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130F ARG* 3.3 47.2 + - + +
162F TYR* 2.6 23.6 + - - -
186F ARG* 3.1 14.0 + - - -
21G ILE* 3.9 7.5 - - + +
106G VAL* 3.6 27.6 - - + -
110G GLU* 3.8 29.4 - - + +
138G ASN 3.6 20.2 - - - +
139G LEU* 2.9 16.8 + - + +
141G PRO* 1.3 77.4 - - - +
143G ALA* 1.3 55.0 + - - +
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Residues in contact with ALA 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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148F LYS* 2.7 31.0 + - - +
161F ALA* 3.7 2.8 - - - +
162F TYR* 3.7 2.9 - - - -
21G ILE* 3.6 19.3 - - + +
23G VAL* 3.7 22.9 - - + -
139G LEU 3.0 13.4 + - - +
140G VAL 3.1 7.6 + - - +
141G PRO 3.4 0.2 - - - -
142G LEU* 1.3 78.1 - - - +
144G GLU* 1.3 62.1 - - - +
145G SER 3.3 1.7 + - - +
146G VAL* 3.7 12.1 - - + -
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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