Contacts of the strand formed by residues 308 - 311 (chain A) in PDB entry 1ML3
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 SER 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A CYS* 2.9 30.1 + - - -
173A PRO* 4.3 10.5 - - - -
174A ILE* 3.8 6.9 - - - +
288A ILE 3.1 4.5 + - - +
289A LEU* 3.4 14.7 - - - -
290A GLY 3.0 23.0 + - - -
306A ARG* 3.3 1.2 - - - +
307A SER* 1.3 80.1 - - - +
309A ILE* 1.3 64.5 + - - +
310A TYR 4.0 0.9 - - - -
331A SER* 2.5 26.2 + - - -
332A TRP 3.5 5.2 - - - -
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Residues in contact with ILE 309 (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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290A GLY 3.3 5.2 - - - +
291A TYR* 4.0 22.4 - - - +
292A THR* 4.4 2.2 - - + +
301A PHE* 3.6 32.5 - - + -
304A ASP* 3.7 37.0 - - + +
306A ARG* 3.8 25.1 - - + +
308A SER* 1.3 77.7 - - - +
310A TYR* 1.3 67.7 + - - +
311A ASP 3.4 0.9 + - - -
331A SER* 3.1 4.9 + - - -
332A TRP* 2.8 60.4 + - - +
333A TYR* 4.0 9.4 - - - -
334A ASP 4.7 1.1 - - - +
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Residues in contact with TYR 310 (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* 4.7 4.5 - - + -
270A ILE* 5.2 0.2 - - - +
273A ILE* 5.4 0.2 - - - +
274A ASP* 2.6 43.8 + - - +
277A LEU* 3.5 43.6 - - + +
278A LYS* 4.5 3.1 - - + -
289A LEU* 4.3 11.5 - - + +
290A GLY 2.8 14.8 + - - +
291A TYR* 3.1 21.8 - + + +
292A THR* 2.8 30.1 + - - +
308A SER 4.0 0.4 - - - -
309A ILE* 1.3 72.0 - - - +
311A ASP* 1.3 65.5 + - - +
312A SER* 3.7 13.8 + - - -
315A THR* 3.0 42.0 - - + +
316A LEU* 4.5 0.2 - - - +
329A ILE* 3.8 10.1 - - + -
330A VAL 3.6 7.6 - - - -
331A SER* 3.3 9.4 + - - +
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Residues in contact with ASP 311 (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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292A THR* 3.8 13.0 - - - +
294A GLU 4.8 1.1 - - - +
301A PHE* 5.2 0.3 - - - -
309A ILE 3.4 0.6 + - - -
310A TYR* 1.3 70.9 - - - +
312A SER* 1.3 63.3 + - - +
313A LYS* 3.6 2.3 + - - +
314A ALA* 2.9 31.0 + - + +
315A THR* 3.0 23.1 + - - -
330A VAL* 2.9 20.8 + - + +
332A TRP* 2.9 33.5 + - + +
212B ARG* 3.0 29.3 + - - -
223B PRO* 4.5 0.5 - - - +
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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