Contacts of the strand formed by residues 274 - 279 (chain A) in PDB entry 3QI5
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 PRO 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ALA* 3.8 31.9 - - + +
259A ALA 3.2 15.3 - - - +
260A ALA 4.2 0.9 - - - +
272A ARG 3.7 3.1 - - - +
273A LYS* 1.4 86.9 - - + +
275A LEU* 1.3 65.8 + - - +
276A ARG 3.6 0.4 - - - -
277A PHE* 3.9 13.3 - - - -
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Residues in contact with LEU 275 (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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96A VAL* 3.8 29.6 - - + -
125A GLU* 3.4 2.3 - - - +
126A ALA* 2.9 34.0 + - + +
128A LEU* 3.7 28.7 - - + -
132A ASP* 4.1 2.0 - - - +
259A ALA 3.1 0.6 + - - -
261A ARG* 3.5 41.6 - - - +
270A TRP* 4.2 0.9 - - + -
273A LYS* 2.9 35.8 + - + +
274A PRO* 1.3 80.4 - - - +
276A ARG* 1.3 58.3 + - - +
277A PHE* 3.3 13.8 - - + -
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 2.7 44.1 + - + +
124A THR 3.5 12.6 - - - +
125A GLU* 3.3 26.9 - - + -
182A ARG* 4.0 0.2 - - - +
257A VAL 3.3 3.0 - - - +
258A ALA* 3.4 3.6 - - - -
259A ALA* 2.7 42.8 + - - +
260A ALA 3.0 27.8 + - - +
261A ARG* 4.0 1.5 - - - +
262A VAL* 3.7 15.9 - - - +
275A LEU* 1.3 78.4 - - - +
277A PHE* 1.3 65.0 + - - +
278A TYR* 3.6 18.7 - - + -
287A VAL* 2.9 36.9 + - - +
289A ASP* 3.8 26.7 + - - +
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Residues in contact with PHE 277 (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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96A VAL* 3.8 23.8 - - + -
99A ALA* 3.7 29.8 - - + +
100A ARG* 3.7 40.4 - - + -
103A LEU* 3.6 11.7 - - + +
123A GLU* 3.4 2.9 - - - -
124A THR* 2.9 39.7 + - - +
126A ALA* 4.2 7.4 - - + -
256A VAL* 4.0 12.8 - - + -
257A VAL 3.2 4.0 - - - -
258A ALA* 3.9 20.2 - - + -
274A PRO 3.9 17.0 - - - -
275A LEU* 3.3 24.9 - - + -
276A ARG* 1.3 77.3 - - - +
278A TYR* 1.3 61.6 + - - +
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Residues in contact with TYR 278 (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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103A LEU* 4.3 7.3 - - - +
122A VAL 3.1 13.2 - - - +
123A GLU* 3.8 9.0 - - + -
256A VAL* 3.8 1.6 - - - -
257A VAL* 2.9 58.9 + - + +
259A ALA* 4.1 7.0 - - + -
276A ARG* 3.6 39.0 - - + -
277A PHE* 1.3 75.9 - - - +
279A VAL* 1.3 78.5 + - - +
280A ARG 3.3 0.2 + - - -
281A GLY 5.3 0.7 - - - -
285A VAL* 3.8 22.9 - - + -
287A VAL 4.4 1.6 - - - -
288A VAL* 4.8 5.2 - - + -
289A ASP* 2.9 37.8 + - - +
293A GLU* 3.4 24.5 + - - -
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Residues in contact with VAL 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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103A LEU* 4.5 8.3 - - + -
104A GLY* 5.2 1.6 - - - +
121A ILE 4.7 1.3 - - - +
122A VAL* 3.0 32.2 + - + +
251A PRO* 4.2 29.4 - - + -
255A ALA* 3.8 11.0 - - + +
256A VAL* 5.2 0.2 - - - +
278A TYR* 1.3 80.4 - - - +
280A ARG* 1.3 73.9 + - - +
281A GLY 3.3 0.9 + - - -
282A SER* 3.3 31.7 + - - -
285A VAL* 4.0 0.2 - - - +
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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