Contacts of the strand formed by residues 314 - 318 (chain A) in PDB entry 1MRA
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 HIS 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL* 4.2 8.9 - - - +
135A GLN* 2.7 32.3 - - - +
218A THR* 6.0 1.8 - - + -
219A TRP* 3.8 13.4 - + - -
266A LEU* 3.9 27.5 - - + +
293A PRO* 4.0 14.3 + - + +
294A MET 2.9 21.2 + - - +
295A SER* 2.9 20.3 + - - +
307A LEU* 4.6 1.8 - - - +
312A THR 4.2 0.9 - - - +
313A ALA* 1.3 75.5 - - - +
315A TRP* 1.3 79.9 + + - +
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Residues in contact with TRP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.7 0.2 - - - -
135A GLN* 3.5 46.3 + - + -
136A ALA 3.1 37.2 - - - -
137A TYR* 3.8 22.6 - + + -
161A ARG* 4.8 13.2 - - + -
162A ALA* 4.0 18.2 - - + -
191A GLY* 6.2 0.4 - - - -
193A MET* 3.6 21.0 - - + +
218A THR* 5.1 4.0 - - + +
219A TRP* 3.9 9.9 - + + -
295A SER* 3.0 27.0 + - - +
296A SER 3.1 10.2 + - - +
307A LEU* 3.8 6.1 - - - +
314A HIS* 1.3 116.6 + + - +
316A LEU* 1.3 58.8 + - - +
335A GLY 5.3 0.2 - - - -
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.3 8.2 - - + +
135A GLN 2.9 12.5 + - - +
136A ALA* 2.9 39.2 - - + +
137A TYR* 2.9 10.5 + - - -
296A SER* 3.9 9.6 - - - +
300A GLN* 3.7 24.7 - - + +
303A SER 4.2 1.8 - - - -
304A ALA* 3.6 40.6 - - + +
307A LEU* 3.8 12.5 - - + +
315A TRP* 1.3 72.8 - - - +
317A GLU* 1.3 83.6 + - - +
318A ARG* 3.8 2.9 - - - +
330A LEU* 5.0 0.7 - - + -
332A PHE* 4.4 5.4 - - + -
337A ALA* 4.0 12.8 - - + -
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Residues in contact with GLU 317 (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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137A TYR* 3.2 29.2 - - + +
139A SER* 2.7 31.1 + - - -
164A LYS* 3.0 6.8 + - - -
296A SER* 3.5 17.4 + - - +
297A HIS* 3.2 14.1 - - - -
298A LEU* 3.0 30.2 + - - +
300A GLN* 3.8 9.7 + - - +
315A TRP 4.1 1.0 + - - -
316A LEU* 1.3 85.1 - - - +
318A ARG* 1.3 65.6 + - - +
319A LEU* 3.5 10.9 + - + +
399A APG 2.5 25.7 - - - +
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Residues in contact with ARG 318 (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 ALA* 4.7 1.3 - - + -
137A TYR 2.9 21.1 + - - +
138A ASP* 2.7 40.3 + - - +
139A SER* 2.9 33.3 + - - +
158A LEU* 6.2 1.8 - - - +
160A PHE* 3.5 32.4 - - + -
300A GLN* 3.3 14.8 - - - +
316A LEU* 3.7 2.5 + - - -
317A GLU* 1.3 70.3 - - - +
319A LEU* 1.3 62.7 + - - +
320A ASP* 4.9 13.7 + - - +
332A PHE* 3.7 36.8 - - + -
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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