Contacts of the strand formed by residues 278 - 289 (chain A) in PDB entry 1QVJ
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 ALA 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ARG* 4.0 18.8 - - + +
162A LEU* 3.3 18.2 - - + +
164A ARG 3.3 25.4 - - - +
166A GLY 3.2 7.4 - - - -
275A THR* 2.8 35.1 + - - +
277A ASN* 1.3 78.5 - - - +
279A TRP* 1.3 64.2 + - - +
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Residues in contact with TRP 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A SER* 4.8 0.4 - - - -
140A TYR* 3.7 33.2 - + - -
147A PRO* 3.9 8.1 - - + -
148A ARG 3.8 2.9 - - - -
149A ASN* 3.6 32.8 - - + +
150A PRO* 3.5 20.5 - - + +
162A LEU* 3.2 9.7 - - - +
166A GLY* 2.9 26.9 + - - -
167A PRO* 3.7 20.1 - - + +
168A ASN* 2.9 26.7 + - - -
268A TYR* 3.5 35.2 - + + -
274A ASN* 3.3 14.8 - - - +
277A ASN 3.9 3.8 - - - -
278A ALA* 1.3 83.1 - - - +
280A MSE 1.3 67.6 + - - +
281A GLU* 2.8 29.4 + - + +
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Residues in contact with MSE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 4.7 9.0 - - + -
168A ASN* 3.5 25.4 - - - +
170A ALA* 3.8 17.7 - - + -
216A MSE 3.4 31.9 - - - +
268A TYR* 4.1 0.3 - - - -
269A VAL* 3.1 26.9 + - + +
271A ASP* 3.6 34.3 - - + +
273A ARG* 3.6 29.6 - - + +
274A ASN* 2.8 14.4 + - - +
279A TRP* 1.3 78.7 - - - +
281A GLU* 1.3 65.4 + - - +
554A RP5 4.1 15.0 - - - +
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A SER* 2.5 27.0 + - - -
136A LYS* 2.8 29.7 + - + +
137A ASN* 4.2 2.3 - - - +
150A PRO* 5.2 0.7 - - - +
167A PRO* 3.6 12.4 - - + +
168A ASN 3.0 8.3 + - - +
169A HIS* 3.3 23.8 - - + +
170A ALA* 2.9 27.3 + - - +
267A GLY* 3.2 16.4 - - - +
268A TYR 3.7 7.6 - - - +
269A VAL* 4.5 2.7 - - - +
279A TRP* 2.8 30.4 + - + +
280A MSE 1.3 79.5 - - - +
282A THR* 1.3 62.1 + - - +
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Residues in contact with THR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 4.4 4.9 - - - +
170A ALA* 3.4 18.1 + - - +
171A ALA* 3.8 0.5 + - - -
172A ASP* 2.6 32.8 + - - +
265A TYR* 4.1 7.4 - - + -
266A LYS* 3.2 5.0 - - - +
267A GLY 2.9 31.1 + - - -
269A VAL* 3.7 22.9 - - + +
281A GLU* 1.3 77.2 - - - +
283A GLU* 1.3 65.6 + - - +
284A ALA 4.3 2.7 - - - +
327A PHE* 3.8 20.0 - - + -
554A RP5 4.1 7.0 - - - +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LYS* 2.6 41.0 + - - +
170A ALA 3.4 7.6 + - - +
171A ALA* 3.5 2.8 - - - -
172A ASP 3.0 21.9 + - - -
223A ILE* 3.8 23.0 - - + +
227A LEU* 4.1 2.4 - - - +
263A VAL* 4.4 11.2 - - + +
265A TYR 3.3 3.6 - - - -
266A LYS* 3.8 31.5 + - + +
282A THR* 1.3 77.0 + - - +
284A ALA* 1.3 60.7 + - - +
285A VAL* 3.7 20.5 + - + +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ASP* 3.4 15.7 - - + +
174A ILE* 4.4 6.3 - - + -
263A VAL* 3.8 1.4 - - - +
264A ILE* 2.7 39.4 + - + -
265A TYR* 2.8 23.3 + - + +
282A THR 4.0 0.2 - - - -
283A GLU* 1.3 74.9 - - - +
285A VAL* 1.3 56.2 + - - +
327A PHE* 3.9 34.5 - - + -
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ASP 3.0 8.2 + - - +
173A PRO* 3.7 3.3 - - - +
174A ILE* 2.9 26.8 + - - +
223A ILE* 5.4 0.2 - - + -
227A LEU* 3.8 21.5 - - + -
261A HIS* 3.4 34.8 - - + -
262A LEU 3.4 8.3 - - - +
263A VAL* 4.5 7.4 - - + -
264A ILE* 4.7 0.4 - - - -
283A GLU* 3.9 25.6 - - + +
284A ALA* 1.3 79.8 - - - +
286A ASN* 1.3 63.9 + - - +
287A TYR* 3.6 25.5 - - + +
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Residues in contact with ASN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ILE* 2.9 25.5 + - + +
176A THR* 3.0 28.7 + - - +
261A HIS* 3.2 7.2 - - - -
262A LEU* 2.8 42.1 + - + +
264A ILE* 3.9 18.2 - - + +
285A VAL* 1.3 72.0 - - - +
287A TYR* 1.3 66.6 + - - +
331A VAL* 3.4 22.3 - - + +
335A ARG* 2.9 35.4 + - - +
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Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PRO* 5.1 1.1 - - + -
174A ILE 3.1 4.4 + - - -
175A ILE* 3.3 17.5 - - + +
176A THR 3.1 22.5 + - - +
224A SER* 5.3 4.9 - - - -
227A LEU* 3.5 24.0 - - + +
256A LEU* 3.8 28.2 - - + +
257A PHE* 3.4 70.3 + + - +
259A GLN* 4.9 0.9 - - - -
260A ASP 5.6 0.7 - - - -
261A HIS* 3.6 30.3 + + + +
285A VAL* 3.6 35.5 - - + +
286A ASN* 1.3 73.6 + - - +
288A HIS* 1.3 59.7 + - - +
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Residues in contact with HIS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A THR* 2.9 24.8 + - - +
177A ARG* 4.4 2.2 - - - -
178A TRP* 3.4 24.3 + + - -
197A LEU* 3.6 20.4 - - + +
256A LEU* 4.1 10.8 + - - +
259A GLN* 3.5 23.2 + - - +
286A ASN* 3.8 2.4 + - - +
287A TYR* 1.3 73.4 - - - +
289A ASP* 1.3 66.5 + - - +
290A GLU* 3.0 42.3 + - + -
294A ILE* 5.4 1.2 - - - +
335A ARG* 3.4 48.7 - - - +
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Residues in contact with ASP 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A THR 2.9 16.6 + - - +
177A ARG* 3.8 19.3 - - + +
178A TRP 4.4 1.6 + - - -
180A ARG* 5.4 0.2 + - - -
256A LEU* 4.3 8.2 - - + +
288A HIS* 1.3 75.5 - - - +
290A GLU* 1.3 63.2 + - - +
291A THR* 3.5 5.0 + - - -
292A GLY* 2.8 31.7 + - - -
293A GLU 3.6 3.1 + - - -
294A ILE* 3.0 25.6 + - - +
295A MSE 2.6 45.2 + - + +
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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