Contacts of the strand formed by residues 372 - 377 (chain A) in PDB entry 1ML0
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 GLN 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.7 5.9 - - - +
211A LEU* 3.5 8.1 - - + -
248A THR* 2.9 35.8 + - - +
253A PRO* 3.5 27.4 - - + +
255A GLN* 3.4 32.1 + - - +
257A ALA* 4.8 1.6 - - - +
284A LEU* 5.6 0.4 - - - +
367A LEU 3.6 2.3 - - - +
368A MET* 3.6 1.2 - - - -
369A LEU* 2.7 55.5 + - + +
370A GLU 4.3 1.9 + - - +
371A GLY* 1.3 85.1 - - - +
373A GLN* 1.3 62.4 + - - +
374A TYR* 3.1 25.6 + - + +
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Residues in contact with GLN 373 (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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16A VAL* 4.5 4.3 - - + -
68A VAL* 4.6 2.1 - - - +
70A ASN* 3.2 22.8 + - - +
92A PRO* 2.9 28.9 + - - +
93A PHE 4.4 1.0 + - - -
94A PRO* 3.9 15.6 - - + +
194A TRP* 3.2 19.3 + - - -
211A LEU 3.0 7.1 + - - +
212A SER* 3.3 21.0 + - - +
213A ALA 2.8 27.6 + - - +
366A SER* 5.6 1.1 - - - -
367A LEU 3.3 4.7 - - - +
368A MET* 3.7 23.2 - - + +
372A GLN* 1.3 76.8 - - - +
374A TYR* 1.3 75.3 + - - +
375A ARG* 5.1 2.9 - - + +
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Residues in contact with TYR 374 (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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211A LEU* 3.7 15.5 - - + +
213A ALA* 3.4 27.4 - - + -
215A SER* 6.4 1.1 - - - -
247A LEU* 3.5 55.5 + - + -
249A PRO* 3.6 13.4 - - + +
257A ALA* 4.4 11.2 - - + -
365A VAL 3.7 1.0 - - - +
366A SER* 3.1 7.9 - - - -
367A LEU* 3.0 45.3 + - + +
369A LEU* 5.3 1.1 - - + -
372A GLN* 3.1 41.7 + - + -
373A GLN* 1.3 88.2 - - - +
375A ARG* 1.3 60.0 + - - +
376A LEU* 3.7 18.2 + - + +
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Residues in contact with ARG 375 (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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93A PHE* 2.9 24.6 + - - +
94A PRO* 3.2 22.9 - - + +
95A SER* 3.2 23.1 + - - -
96A VAL* 3.3 18.6 - - - +
164A ASP* 3.1 37.1 + - - -
165A VAL* 3.6 15.6 - - - +
213A ALA 2.8 17.2 + - - +
214A ARG* 3.9 21.3 - - + +
215A SER 2.7 31.8 + - - +
365A VAL 3.9 2.2 - - - -
366A SER* 4.0 3.1 - - - +
373A GLN* 5.1 2.9 - - - +
374A TYR* 1.3 72.1 - - - +
376A LEU* 1.3 59.9 + - - +
377A GLU* 3.2 29.5 + - + +
379A PHE* 5.6 0.4 - - - -
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Residues in contact with LEU 376 (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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215A SER* 3.4 9.4 - - - +
217A VAL* 3.9 17.5 - - + -
247A LEU* 4.5 17.0 - - + -
259A MET* 4.1 22.2 - - + -
260A ASN 6.1 0.2 - - - +
281A LEU 4.5 2.2 - - - +
282A ALA* 4.5 16.2 - - + -
364A GLY* 3.0 25.3 - - - -
365A VAL* 2.8 38.6 + - + +
367A LEU* 5.9 3.6 - - + +
374A TYR* 4.0 24.7 - - + +
375A ARG* 1.3 77.9 - - - +
377A GLU* 1.3 60.9 + - - +
378A TYR* 3.9 12.1 - - - +
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Residues in contact with GLU 377 (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* 3.6 11.1 - - - +
214A ARG* 2.7 43.4 + - + +
215A SER 2.8 14.9 + - - +
216A PRO* 3.5 6.9 - - + +
217A VAL* 2.7 32.8 + - - +
218A CYS 3.8 0.9 + - - -
363A VAL 3.7 4.4 - - - +
364A GLY* 5.5 1.6 - - - -
375A ARG* 3.2 35.5 + - + +
376A LEU* 1.3 77.2 - - - +
378A TYR* 1.3 59.5 + - - +
379A PHE* 3.0 41.2 + - + +
382A HIS* 4.4 4.3 - - - +
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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