Contacts of the strand formed by residues 142 - 153 (chain F) in PDB entry 6Q2J
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 CYS 142 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F PHE* 4.0 4.7 - - - -
34F ASP* 4.6 3.3 - - - +
124F LYS* 4.0 7.6 - - - -
125F VAL 3.6 8.1 - - - -
126F PHE* 3.5 29.6 - - + -
136F GLU 5.1 0.9 - - - +
137F CYS* 2.0 59.4 - - - -
138F GLN 2.9 20.2 + - - +
139F TRP* 3.8 8.3 + - - +
141F GLY* 1.3 78.5 - - - +
143F ALA* 1.3 71.7 + - - +
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Residues in contact with ALA 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F PHE* 3.6 40.8 - - + -
33F ARG 5.0 0.2 - - - +
34F ASP 3.7 13.9 - - - +
36F TYR* 4.5 13.9 - - + -
125F VAL* 2.9 36.4 + - + +
142F CYS* 1.3 80.1 - - - +
144F ARG* 1.3 64.1 + - - +
145F VAL* 4.0 0.5 - - - +
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Residues in contact with ARG 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D ASN* 3.4 45.6 + - - +
260D SER* 6.3 0.2 - - - -
261D THR* 5.2 2.8 - - - +
34F ASP* 3.8 9.9 + - - +
35F ALA* 3.2 36.1 - - + +
36F TYR* 3.5 1.7 + - - -
77F ARG* 4.7 7.5 - - - +
122F TYR* 4.1 21.6 + - + -
123F LEU 3.1 14.6 - - - +
124F LYS* 4.3 0.9 - - - +
137F CYS* 2.4 57.8 + - - +
138F GLN* 5.7 1.6 - - - +
143F ALA* 1.3 74.9 - - - +
145F VAL* 1.3 59.8 + - - +
146F TYR* 3.2 34.8 - - + -
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Residues in contact with VAL 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F TYR* 4.0 32.3 - - + +
51F LEU* 4.4 10.1 - - + -
53F VAL* 4.9 5.2 - - + -
95F LEU* 3.8 26.2 - - + -
122F TYR* 3.2 2.4 - - - -
123F LEU* 2.9 34.2 + - + +
125F VAL* 3.7 26.5 - - + -
143F ALA 4.0 2.0 - - - +
144F ARG* 1.3 78.2 - - - +
146F TYR* 1.3 74.6 + - - +
147F PHE* 3.7 13.9 - - + -
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Residues in contact with TYR 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D ASN 2.7 28.8 + - - -
258D CYS* 3.2 21.3 - - + +
261D THR* 3.4 28.3 - - + +
35F ALA* 4.3 2.5 - - + -
36F TYR 3.4 16.8 + - - +
37F TRP* 3.4 43.7 - + + -
38F GLU 3.6 14.2 + - - -
120F THR* 5.2 8.1 - - + -
121F VAL 3.7 3.8 - - - +
122F TYR* 3.4 27.6 - + + -
144F ARG* 3.2 29.0 - - + -
145F VAL* 1.3 81.2 - - - +
147F PHE* 1.3 74.3 + - - +
148F SER 4.3 0.2 - - - -
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Residues in contact with PHE 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F GLU* 3.3 34.3 - - + +
40F LEU* 3.7 27.8 - - + -
50F LEU* 3.9 15.7 - - + -
51F LEU* 5.3 0.9 - - + -
72F LEU* 6.0 0.7 - - + -
86F ILE* 3.6 29.4 - - + -
95F LEU* 4.0 13.7 - - + -
120F THR* 3.6 3.0 - - - -
121F VAL* 2.9 53.1 + - + +
122F TYR* 4.6 3.1 - - - -
123F LEU* 3.7 17.5 - - + -
145F VAL* 3.7 29.6 - - + -
146F TYR* 1.3 81.7 - - - +
148F SER* 1.3 63.3 + - - +
149F PHE* 3.6 2.5 + - - +
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Residues in contact with SER 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D LYS* 3.5 22.1 + - - +
37F TRP* 3.5 28.9 - - - -
38F GLU 2.9 12.4 + - - -
39F LYS* 3.4 13.2 - - - -
40F LEU 3.4 15.7 + - - -
119F LEU* 3.4 14.0 + - - -
120F THR* 4.5 1.4 + - - +
146F TYR 4.3 0.2 - - - -
147F PHE* 1.3 68.5 - - - +
149F PHE* 1.3 63.3 + - - +
150F PHE* 3.7 18.7 - - - -
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Residues in contact with PHE 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F LEU* 3.3 22.9 - - + +
41F TYR 3.5 22.2 - - - -
42F VAL* 3.5 17.0 - - + -
101F LEU* 3.7 2.9 - - + -
106F TRP* 3.3 84.4 - + + -
118F LEU 4.3 11.6 - - - +
119F LEU* 3.6 30.8 + - - +
121F VAL 6.2 0.2 - - - +
147F PHE 3.6 4.8 + - - +
148F SER* 1.3 75.5 - - - +
150F PHE* 1.3 82.9 + - - +
151F ASN* 4.2 11.0 - - + -
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Residues in contact with PHE 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D LYS* 6.3 2.2 - - - -
39F LYS* 3.8 33.9 - - + -
40F LEU 3.1 6.8 + - - -
41F TYR* 3.6 37.5 - + + -
42F VAL 3.8 1.2 + - - -
119F LEU* 5.2 11.2 - - + -
148F SER* 3.7 23.3 - - - -
149F PHE* 1.3 100.2 - - - +
151F ASN* 1.3 62.0 + - - +
152F THR* 3.2 16.9 + - + +
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Residues in contact with ASN 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F VAL* 3.3 14.6 - - - +
103F HIS* 3.9 25.0 + - - -
106F TRP* 5.8 1.7 - - - +
107F GLU* 5.6 4.0 + - - -
149F PHE* 4.2 10.3 - - + -
150F PHE* 1.3 71.9 - - - +
152F THR* 1.3 64.1 + - + +
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Residues in contact with THR 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F TYR* 3.8 12.5 - - - +
42F VAL* 3.0 25.0 + - - -
150F PHE* 3.2 7.9 - - + +
151F ASN* 1.3 84.7 - - + +
153F SER* 1.3 70.8 + - - +
155F PRO* 5.7 0.5 - - - +
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Residues in contact with SER 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F TYR* 4.1 4.9 - - - -
42F VAL* 3.5 26.9 + - - +
43F ASP* 4.6 6.7 + - - +
152F THR* 1.3 89.8 + - - +
154F PHE* 1.3 68.9 + - - +
155F PRO* 3.4 6.8 - - - +
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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