Contacts of the strand formed by residues 268 - 274 (chain A) in PDB entry 1MAQ
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 GLY 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A PHE* 3.5 16.3 - - - -
104A GLN* 4.0 0.7 - - - +
105A GLY 2.8 29.3 + - - -
107A SER* 3.8 5.8 - - - -
111A SER* 3.7 2.2 - - - -
254A GLN 3.0 17.5 - - - -
256A TYR* 4.1 8.1 - - - -
267A ALA* 1.3 75.1 - - - +
269A ALA* 1.3 63.2 + - - +
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Residues in contact with ALA 269 (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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79A PHE* 4.2 7.2 - - + -
83A SER* 4.2 9.9 - - - +
102A THR* 3.7 21.3 - - + -
103A VAL 3.3 13.2 - - - +
111A SER* 3.4 9.1 + - - -
252A LEU 3.8 0.7 - - - +
253A SER* 3.5 2.3 - - - -
254A GLN* 2.8 56.2 + - - +
268A GLY* 1.3 76.4 - - - +
270A PHE* 1.3 59.4 + - - +
271A THR 4.3 0.2 + - - -
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Residues in contact with PHE 270 (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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101A VAL 3.7 0.9 - - - +
102A THR* 3.4 1.2 - - - -
103A VAL* 2.9 41.5 + - + +
105A GLY* 4.8 0.6 - - - +
111A SER* 3.6 32.2 - - - +
114A VAL* 4.3 12.3 - - + -
115A GLY* 3.3 30.7 - - - -
118A PHE* 4.5 6.1 - + - -
119A LEU* 5.8 0.7 - - + -
220A TYR* 3.6 20.2 - + - -
251A VAL* 3.9 22.9 - - + -
252A LEU 3.3 19.1 - - - -
253A SER 4.6 0.4 - - - -
269A ALA* 1.3 71.9 - - - +
271A THR* 1.3 61.7 + - - +
272A VAL* 3.4 31.4 - - + -
287A LEU* 4.3 19.4 - - + +
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Residues in contact with THR 271 (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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84A ALA* 5.1 2.4 - - + -
88A LEU* 5.0 7.2 - - + -
100A TYR* 4.4 5.6 - - + -
101A VAL 3.0 10.8 - - - +
102A THR* 3.0 27.2 + - - +
251A VAL* 3.3 5.7 - - - +
252A LEU* 2.8 56.5 + - + +
254A GLN* 4.4 11.3 + - - -
269A ALA 4.9 0.2 - - - -
270A PHE* 1.3 76.8 - - - +
272A VAL* 1.3 68.8 + - - +
273A ILE* 4.0 24.5 - - + -
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Residues in contact with VAL 272 (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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100A TYR* 3.4 5.2 - - - +
101A VAL* 2.9 36.5 + - + +
118A PHE* 4.4 16.4 - - + -
250A VAL 4.0 2.7 - - - -
251A VAL* 3.9 15.9 - - + -
270A PHE* 3.4 35.0 - - + -
271A THR* 1.3 73.0 - - - +
273A ILE* 1.3 71.4 + - - +
274A CYS* 3.7 14.4 + - - -
283A VAL* 4.4 15.9 - - + -
287A LEU* 4.5 5.6 - - + -
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Residues in contact with ILE 273 (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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88A LEU* 4.4 14.8 - - + -
94A ALA* 4.7 10.5 - - + -
99A ARG* 3.0 39.7 - - - +
100A TYR* 3.7 23.6 - - + -
244A ILE* 4.0 26.7 - - + -
249A ASP* 3.3 23.2 - - - +
250A VAL* 3.0 30.9 + - + +
271A THR* 4.0 13.7 - - + -
272A VAL* 1.3 77.0 - - - +
274A CYS* 1.3 60.1 + - - +
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Residues in contact with CYS 274 (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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99A ARG* 2.8 46.6 + - - +
101A VAL* 4.4 2.7 - - - -
249A ASP* 4.2 5.8 - - - -
272A VAL* 4.0 18.8 - - - -
273A ILE* 1.3 75.4 - - - +
275A ARG* 1.3 61.3 + - - +
276A ASP 3.6 14.1 - - - +
279A GLU* 3.5 15.3 - - + +
280A ALA* 3.7 22.9 - - - +
283A VAL* 3.9 24.9 - - - -
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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