Contacts of the strand formed by residues 148 - 155 (chain B) in PDB entry 1QXP
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 GLU 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU 4.8 1.5 - - - +
19B GLY* 3.6 19.1 - - - +
25B ILE* 2.3 36.2 - - + +
144B TRP* 3.3 3.1 - - - -
145B GLN* 2.8 46.2 + - + +
146B PHE 4.8 2.7 - - - +
147B GLY* 1.4 71.3 - - - +
149B TRP* 1.3 66.3 + - - +
150B VAL* 3.3 7.7 + - + -
362B GLU* 5.1 7.0 - - - +
416B LYS* 4.4 14.1 + - - +
418B ARG* 5.5 3.1 + - - -
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Residues in contact with TRP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLY* 3.0 17.2 + - - +
20B SER* 4.1 3.4 - - - +
21B HIS* 3.3 48.3 - + + +
24B ALA* 3.1 25.3 - - + +
25B ILE* 3.1 16.8 + - - +
123B ARG* 3.8 27.5 - - + +
124B VAL* 5.5 0.2 - - + -
142B GLN* 3.9 31.0 - - + +
143B LEU 3.9 14.8 - - - -
144B TRP* 3.6 26.8 - + + +
148B GLU* 1.3 72.5 - - - +
150B VAL* 1.3 60.4 + - - +
206B ASP 4.8 0.9 - - - -
207B PHE 4.3 9.6 - - - -
208B THR 3.3 35.0 - - - -
209B GLY* 3.7 11.7 - - - -
343B LEU* 5.1 8.6 - - + +
345B PRO* 6.0 1.6 - - - +
346B ASP* 4.7 0.2 - - - -
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA* 4.5 0.2 - - - -
25B ILE* 3.8 24.7 - - + +
27B TYR* 3.5 45.3 - - + +
141B PHE 3.4 0.5 - - - +
142B GLN* 3.2 5.2 - - - +
143B LEU* 2.9 43.3 + - + +
145B GLN* 4.4 22.9 - - + -
148B GLU* 3.3 7.9 + - + +
149B TRP* 1.3 76.7 - - - +
151B ASP* 1.3 62.5 + - - +
152B VAL* 3.8 7.1 + - + +
188B VAL* 5.5 0.7 - - + -
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Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA* 4.1 11.4 - - + +
25B ILE 3.0 14.7 + - - +
26B LYS* 4.0 11.5 - - + +
27B TYR* 3.1 26.5 + - - +
30B GLN 5.3 4.4 - - - +
32B TYR* 4.6 7.1 + - - +
140B HIS* 2.7 40.5 + - - +
141B PHE 3.8 2.3 - - - -
142B GLN* 3.1 27.0 - - + +
150B VAL* 1.3 74.9 - - - +
152B VAL* 1.3 61.8 + - - +
153B VAL* 4.7 1.9 + - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TYR* 3.8 16.2 - - + -
140B HIS* 3.0 6.5 - - - -
141B PHE* 2.8 40.7 + - - +
143B LEU* 5.1 5.8 - - + -
150B VAL* 4.2 7.4 - - + +
151B ASP* 1.3 80.1 + - - +
153B VAL* 1.3 74.5 + - - +
154B VAL* 4.9 0.2 - - - +
184B ALA* 3.9 26.7 - - + +
187B LYS* 4.1 16.6 - - + +
188B VAL* 3.8 25.8 - - + -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TYR* 5.8 0.2 - - - +
30B GLN* 4.1 36.5 - - + +
31B ASP 4.4 3.4 - - - -
32B TYR* 3.7 40.8 - - + +
35B LEU* 4.6 1.6 - - + -
46B PHE* 4.1 20.9 - - + -
48B ASP* 3.8 1.5 - - - +
138B ILE* 4.2 11.7 - - + -
139B PHE 3.4 8.1 - - - +
140B HIS* 3.9 1.3 - - + -
151B ASP* 5.1 2.2 - - - +
152B VAL* 1.3 74.5 - - - +
154B VAL* 1.3 67.7 + - - +
187B LYS* 3.2 25.5 - - - +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 4.3 4.3 - - - -
48B ASP* 3.3 18.8 - - - +
51B PHE* 5.1 0.4 - - + -
138B ILE* 3.2 5.9 - - - +
139B PHE* 2.9 37.6 + - + +
141B PHE* 4.9 5.8 - - + -
152B VAL 4.9 1.6 - - - +
153B VAL* 1.3 79.4 - - - +
155B ASP* 1.4 69.4 + - - +
180B LEU* 4.4 20.9 - - + +
183B LYS* 3.9 26.0 - - + +
184B ALA* 4.4 15.3 - - + +
187B LYS* 4.3 9.0 - - + -
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Residues in contact with ASP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 3.6 25.1 - - + +
47B GLN* 4.1 2.1 + - - -
48B ASP* 2.7 35.2 + - - +
51B PHE 4.7 1.2 - - - +
53B PRO* 5.0 5.5 - - - +
77B ARG* 4.5 2.2 - - - +
137B GLY 3.5 13.9 - - - +
139B PHE* 5.2 0.4 - - - -
154B VAL* 1.4 87.4 - - - +
156B ASP* 1.4 58.9 + - - +
157B LEU* 2.6 33.9 + - - +
180B LEU* 4.1 0.2 - - - +
183B LYS* 2.6 41.5 + - - +
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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