Contacts of the strand formed by residues 140 - 151 (chain P) in PDB entry 2W2Q
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 VAL 140 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62P ALA* 3.8 30.0 + - + +
80P VAL* 3.9 10.1 - - + -
81P VAL 4.1 1.3 - - - +
82P LEU* 3.7 19.1 - - + -
83P LYS* 3.9 12.9 + - - -
94P THR* 4.5 1.3 - - + -
134P ALA 3.6 19.5 - - - +
135P LEU 4.6 0.7 - - - +
137P LEU* 3.5 30.7 + - + +
138P PRO 3.1 2.4 - - - +
139P HIS* 1.3 76.8 - - - +
141P ASP* 1.3 62.7 + - - +
142P TYR 3.9 10.3 - - - +
143P ILE* 4.1 22.0 - - + -
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Residues in contact with ASP 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ARG* 4.2 11.1 + - - -
61P THR 4.4 2.4 - - - +
62P ALA* 3.5 18.9 - - - -
63P THR* 3.7 2.6 + - - -
81P VAL* 2.8 16.9 + - - +
82P LEU 3.8 17.5 - - - +
83P LYS* 3.9 20.2 - - + +
84P GLU 5.3 1.0 + - - -
139P HIS 3.3 2.0 + - - -
140P VAL* 1.3 73.9 - - - +
142P TYR* 1.3 85.6 + - + +
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Residues in contact with TYR 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ARG* 3.4 45.3 + - + +
296A VAL* 3.5 33.7 + - + +
299A ALA* 3.8 16.1 - - - +
62P ALA* 4.9 0.2 - - - -
63P THR* 3.3 17.5 - - - +
65P HIS* 3.7 24.0 - + - +
81P VAL* 2.8 65.0 + - + +
119P LEU* 5.4 0.2 - - - +
140P VAL* 3.8 3.7 - - - +
141P ASP* 1.3 96.5 - - + +
143P ILE* 1.3 71.5 + - - +
144P GLU* 4.3 4.9 - - + -
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Residues in contact with ILE 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P THR 2.9 6.3 + - - +
64P PHE* 3.3 11.0 - - + -
65P HIS* 2.7 32.7 + - - -
78P TYR* 3.7 26.5 - - + -
79P VAL 3.5 6.7 - - - +
80P VAL* 4.1 19.5 - - + -
126P MET* 5.8 0.2 - - + -
131P LEU* 4.0 18.4 - - + -
134P ALA* 3.7 38.8 - - + +
135P LEU* 3.6 28.3 - - + +
140P VAL* 4.1 6.7 - - + -
142P TYR* 1.3 82.3 - - - +
144P GLU* 1.3 57.4 + - - +
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Residues in contact with GLU 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A VAL* 4.4 4.4 - - + +
293A TYR 4.9 0.5 - - - +
294A SER* 2.3 33.5 + - - -
295A ARG* 3.2 14.2 + - - +
296A VAL* 2.8 43.8 + - + +
65P HIS* 3.3 18.8 - - + +
66P ARG* 5.2 2.5 - - - -
78P TYR* 3.3 2.3 - - - -
79P VAL* 2.8 42.5 + - + +
142P TYR* 4.3 6.0 - - + -
143P ILE* 1.3 75.4 - - - +
145P GLU* 1.3 76.0 + - - +
146P ASP* 3.6 0.8 + - - -
147P SER* 4.9 4.0 + - - -
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Residues in contact with GLU 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A VAL* 5.9 0.2 - - - +
64P PHE* 3.7 20.6 - - + -
65P HIS 2.8 16.9 + - - +
66P ARG* 4.0 12.3 - - + +
67P CYS 4.8 1.2 + - - -
73P ARG* 2.8 61.2 + - - +
74P LEU 3.8 13.7 + - - +
75P PRO* 3.6 21.8 - - + +
77P THR 3.5 5.2 - - - +
78P TYR* 3.6 19.5 + - + -
144P GLU* 1.3 83.7 - - - +
146P ASP* 1.3 70.3 + - - +
147P SER* 4.3 5.4 + - - -
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Residues in contact with ASP 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A THR* 3.7 8.5 - - - +
261A VAL* 3.3 10.9 + - - +
262A SER* 2.7 50.5 + - - -
67P CYS 5.8 0.2 + - - -
74P LEU* 2.8 42.8 + - + +
77P THR* 2.8 36.9 + - + +
78P TYR* 5.4 0.2 - - - -
79P VAL* 5.6 4.2 - - + +
123P LEU* 5.5 0.7 - - + -
144P GLU 3.6 2.9 + - - -
145P GLU* 1.3 80.8 - - - +
147P SER* 1.3 68.0 + - - +
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Residues in contact with SER 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A THR* 3.3 4.2 - - - -
261A VAL* 2.8 46.7 + - - +
292A GLY 5.2 5.1 + - - -
293A TYR 5.7 0.5 + - - -
294A SER* 5.2 1.2 - - - -
67P CYS* 3.8 29.0 + - - +
72P TRP 3.2 15.9 - - - -
73P ARG* 4.4 0.2 - - - -
74P LEU* 3.6 9.1 - - - +
144P GLU* 4.9 4.5 + - - -
145P GLU 4.3 3.8 + - - -
146P ASP* 1.3 80.7 + - - +
148P SER* 1.3 61.8 + - - +
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Residues in contact with SER 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LYS* 4.3 15.4 + - - -
259A GLY 3.3 10.9 + - - -
261A VAL* 4.9 0.2 - - - +
291A GLY* 3.4 18.0 - - - -
292A GLY 4.5 1.4 + - - -
71P PRO 5.3 0.9 + - - -
72P TRP* 2.9 24.6 + - - +
74P LEU* 3.9 17.7 - - - +
147P SER* 1.3 78.6 + - - +
149P VAL* 1.3 62.6 + - - +
150P PHE* 3.5 33.0 - - - -
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Residues in contact with VAL 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LEU* 4.0 11.4 - - + -
258A LYS* 3.5 3.3 - - - +
259A GLY* 2.8 53.0 + - - +
260A THR 3.7 1.6 - - - +
261A VAL* 4.0 26.0 - - + +
264A THR* 3.7 18.6 - - - +
289A LEU* 4.1 20.6 - - + -
290A ALA 3.4 7.2 - - - +
291A GLY* 3.9 13.0 - - - +
297A LEU* 4.6 8.3 - - + -
148P SER* 1.3 76.2 - - - +
150P PHE* 1.3 68.3 + - - +
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Residues in contact with PHE 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LEU* 4.6 0.7 - - - -
256A GLN 6.1 0.4 - - - -
257A GLY 3.5 5.8 - - - +
258A LYS* 3.4 33.0 - - + -
289A LEU* 3.1 6.6 - - - -
290A ALA 2.8 37.0 + - - +
318A PHE* 5.4 2.2 - + + -
72P TRP* 3.3 57.2 - + - -
148P SER* 3.5 26.2 - - - -
149P VAL* 1.3 79.2 - - - +
151P ALA* 1.3 67.2 + - - +
152P GLN* 3.2 14.8 + - - +
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Residues in contact with ALA 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A HIS* 3.5 33.4 - - + +
253A LEU* 3.8 13.9 - - + +
257A GLY* 2.9 27.0 + - - +
288A PRO 3.9 7.4 - - - -
317A ASN* 5.1 0.2 + - - -
150P PHE* 1.3 74.1 - - - +
152P GLN* 1.3 68.3 + - - +
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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