Contacts of the strand formed by residues 20 - 26 (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 GLN 20 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18G ARG 4.7 4.4 + - - +
19G GLY* 1.3 76.5 - - - +
21G ILE* 1.3 62.6 + - - +
22G GLN* 2.9 38.5 + - + +
43G PHE* 5.5 3.6 - - - -
113G ALA* 3.8 5.9 - - - +
117G LYS 3.0 7.2 + - - +
118G THR* 3.8 24.4 + - + +
119G VAL* 2.8 27.7 + - - +
144G GLU* 3.3 32.1 - - + +
145G SER* 5.1 1.4 - - - -
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Residues in contact with ILE 21 (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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186F ARG* 3.7 16.4 - - - +
20G GLN* 1.3 77.9 - - - +
22G GLN* 1.3 65.6 + - - +
23G VAL* 4.0 20.4 - - + -
109G CYS* 3.7 41.1 - - + +
110G GLU* 3.9 12.3 - - - +
113G ALA* 3.7 11.7 - - + -
119G VAL* 3.3 9.4 - - + +
121G VAL* 4.5 7.2 - - + -
139G LEU* 4.7 8.1 - - + -
142G LEU* 3.9 14.8 - - + +
143G ALA* 3.6 9.7 - - + +
144G GLU* 2.8 37.3 + - - +
145G SER 3.4 4.3 + - - -
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Residues in contact with GLN 22 (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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20G GLN* 2.9 38.7 + - + +
21G ILE* 1.3 74.5 - - - +
23G VAL* 1.3 62.9 + - - +
39G ARG* 2.9 41.9 + - - +
43G PHE* 5.0 7.9 - - - -
118G THR* 4.2 8.1 - - - +
119G VAL 2.8 11.8 + - - +
120G ILE* 3.4 19.2 - - + +
121G VAL* 2.8 28.4 + - - +
145G SER* 3.4 17.9 - - - -
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Residues in contact with VAL 23 (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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21G ILE* 4.0 9.6 - - + -
22G GLN* 1.3 78.4 - - - +
24G ILE* 1.3 64.5 + - - +
25G LEU* 3.5 33.9 - - + -
39G ARG* 4.9 2.2 + - - +
121G VAL* 3.5 10.1 - - + +
123G ALA* 5.6 0.4 - - + -
136G ILE* 5.2 2.9 - - + +
139G LEU* 4.0 29.2 - - + -
140G VAL* 5.2 3.1 - - + +
143G ALA* 3.7 24.2 - - + -
145G SER* 2.8 12.7 + - - +
146G VAL* 3.4 11.0 - - + -
147G VAL* 2.9 29.5 + - - +
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Residues in contact with ILE 24 (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* 1.3 73.8 - - - +
25G LEU* 1.3 61.5 + - - +
32G LYS* 3.9 15.4 - - + +
35G GLU* 3.9 13.0 - - + -
36G LEU* 3.7 29.2 - - + +
39G ARG* 3.7 24.2 - - - +
120G ILE* 3.6 28.5 - - + -
121G VAL 2.7 13.6 + - - +
122G ALA* 3.4 2.9 - - + -
123G ALA 3.0 26.3 + - - +
147G VAL* 3.9 6.7 - - + -
149G LEU* 3.7 33.9 - - + -
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Residues in contact with LEU 25 (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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140F VAL* 3.9 26.0 - - + -
146F VAL* 5.9 0.9 - - + -
23G VAL* 3.5 25.6 - - + -
24G ILE* 1.3 75.7 - - - +
26G GLY* 1.3 59.3 + - - +
32G LYS* 3.7 4.1 - - - +
123G ALA* 3.2 14.6 - - + +
125G ASP* 4.1 21.3 - - + -
136G ILE* 4.2 17.3 - - + -
137G LEU* 4.1 9.6 - - + -
140G VAL* 4.5 5.4 - - + -
146G VAL* 4.1 21.5 - - + -
147G VAL 2.8 15.5 + - - +
148G LYS* 3.4 9.4 - - + -
149G LEU* 2.8 30.2 + - - +
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Residues in contact with GLY 26 (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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25G LEU* 1.3 78.9 - - - +
27G PRO* 1.3 76.2 - - - +
30G SER* 3.9 2.7 - - - -
32G LYS* 3.5 8.8 - - - +
123G ALA 3.5 1.0 + - - -
124G LEU* 3.2 19.8 - - - +
125G ASP* 3.2 18.9 + - - +
148G LYS* 4.0 3.8 - - - -
149G LEU 3.6 8.3 - - - -
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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