Contacts of the strand formed by residues 142 - 153 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E PHE* 4.0 5.4 - - - -
34E ASP* 4.6 3.6 - - - +
124E LYS* 4.0 7.6 - - - -
125E VAL 3.6 8.7 - - - -
126E PHE* 3.5 29.6 - - + -
136E GLU 5.1 0.9 - - - +
137E CYS* 2.0 60.4 - - - -
138E GLN 2.9 20.1 + - - +
139E TRP* 3.8 8.7 + - - +
141E GLY* 1.3 77.1 - - - +
143E ALA* 1.3 70.0 + - - +
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Residues in contact with ALA 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PHE* 3.6 41.5 - - + -
34E ASP 3.7 14.1 - - - +
36E TYR* 4.5 14.1 - - + -
125E VAL* 2.9 35.6 + - + +
142E CYS* 1.3 79.5 - - - +
144E ARG* 1.3 64.8 + - - +
145E VAL* 4.1 0.7 - - + +
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Residues in contact with ARG 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C ASN* 3.4 45.8 + - - +
261C THR* 5.2 2.6 - - - +
34E ASP* 3.8 10.1 + - - +
35E ALA* 3.2 36.4 - - + +
36E TYR* 3.5 1.7 + - - -
77E ARG* 4.7 7.7 - - - +
122E TYR* 4.1 21.9 + - + -
123E LEU 3.1 14.8 - - - +
124E LYS* 4.3 0.7 - - - +
137E CYS* 2.4 57.4 + - + +
138E GLN* 5.7 1.4 - - - +
143E ALA* 1.3 74.7 - - - +
145E VAL* 1.3 59.9 + - - +
146E TYR* 3.2 34.5 - - + -
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Residues in contact with VAL 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E TYR* 4.0 33.0 - - + +
51E LEU* 4.4 9.0 - - + -
53E VAL* 4.9 4.3 - - + -
95E LEU* 3.8 26.2 - - + -
122E TYR* 3.2 2.4 - - - -
123E LEU* 2.9 34.8 + - + +
125E VAL* 3.7 26.9 - - + -
143E ALA 4.1 2.2 - - - +
144E ARG* 1.3 77.7 - - - +
146E TYR* 1.3 73.9 + - - +
147E PHE* 3.7 14.0 - - + -
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Residues in contact with TYR 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C ASN 2.7 28.8 + - - -
258C CYS* 3.2 21.0 - - + +
261C THR* 3.4 28.5 - - + +
35E ALA* 4.3 2.2 - - + -
36E TYR 3.4 17.9 + - - +
37E TRP* 3.4 43.9 - + + -
38E GLU 3.6 13.4 + - - -
120E THR* 5.2 9.0 - - + -
121E VAL 3.7 3.4 - - - +
122E TYR* 3.4 28.3 - + + -
144E ARG* 3.2 30.5 - - + -
145E VAL* 1.3 81.8 - - - +
147E PHE* 1.3 74.4 + - - +
148E SER 4.3 0.2 - - - -
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Residues in contact with PHE 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E GLU* 3.3 35.2 - - + +
40E LEU* 3.7 27.8 - - + -
50E LEU* 3.9 15.7 - - + -
51E LEU* 5.3 0.9 - - + -
72E LEU* 6.0 0.4 - - + -
86E ILE* 3.6 31.0 - - + -
95E LEU* 4.0 14.1 - - + -
120E THR* 3.6 3.4 - - - -
121E VAL* 2.9 53.2 + - + +
122E TYR* 4.6 2.9 - - - -
123E LEU* 3.7 16.8 - - + -
145E VAL* 3.7 28.5 - - + -
146E TYR* 1.3 80.5 - - - +
148E SER* 1.3 62.7 + - - +
149E PHE* 3.6 2.9 + - + +
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Residues in contact with SER 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C LYS* 3.5 21.6 + - - +
37E TRP* 3.5 28.9 - - - -
38E GLU 2.9 11.1 + - - -
39E LYS* 3.4 13.2 - - - -
40E LEU 3.4 16.6 + - - -
119E LEU 3.4 13.1 + - - -
120E THR* 4.5 1.2 + - - +
146E TYR 4.3 0.2 - - - -
147E PHE* 1.3 69.0 - - - +
149E PHE* 1.3 63.4 + - - +
150E PHE* 3.7 18.8 - - - -
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Residues in contact with PHE 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU* 3.3 23.6 - - + +
41E TYR 3.5 21.8 - - - -
42E VAL* 3.5 17.0 - - + -
101E LEU* 3.7 2.7 - - + -
106E TRP* 3.3 82.3 - + + -
118E LEU 4.3 10.7 - - - +
119E LEU* 3.6 30.5 + - - +
120E THR 5.8 0.4 - - - +
121E VAL* 5.7 0.4 - - + +
147E PHE 3.6 5.6 + - - +
148E SER* 1.3 73.8 - - - +
150E PHE* 1.3 83.9 + - - +
151E ASN* 4.2 10.5 - - + -
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Residues in contact with PHE 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C LYS* 6.3 1.8 - - - -
39E LYS* 3.8 34.1 - - + -
40E LEU 3.1 6.4 + - - -
41E TYR* 3.6 38.3 - + + -
42E VAL 3.8 1.0 + - - -
119E LEU* 5.2 11.2 - - + -
148E SER* 3.7 22.7 - - - -
149E PHE* 1.3 99.5 - - - +
151E ASN* 1.3 61.6 + - - +
152E THR* 3.2 16.5 + - + +
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Residues in contact with ASN 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E VAL* 3.3 15.0 - - - +
103E HIS* 3.9 25.6 + - - -
106E TRP* 5.8 2.3 - - - +
107E GLU* 5.6 4.0 + - - -
149E PHE* 4.2 9.5 - - + -
150E PHE* 1.3 71.7 - - - +
152E THR* 1.3 64.0 + - + +
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Residues in contact with THR 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E TYR* 3.8 12.5 - - - +
42E VAL* 3.0 25.1 + - - +
150E PHE* 3.2 8.4 - - + +
151E ASN* 1.3 86.0 - - + +
153E SER* 1.3 71.2 + - - +
155E PRO* 5.7 0.3 - - - +
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Residues in contact with SER 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E TYR* 4.1 4.6 - - - -
42E VAL* 3.5 25.8 + - - +
43E ASP* 4.6 6.9 + - - +
152E THR* 1.3 90.5 + - - +
154E PHE* 1.3 70.2 + - - +
155E PRO* 3.4 6.9 - - - +
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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