Contacts of the strand formed by residues 349 - 354 (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 VAL 349 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ASP* 4.7 10.3 - - + +
284A LEU 3.3 8.7 - - - +
285A ALA* 4.5 13.0 - - + -
287A LEU* 3.9 6.2 - - - +
343A GLU* 3.6 5.2 - - - +
344A GLY* 2.7 42.5 + - - -
345A GLN* 4.1 15.7 - - + +
346A SER* 3.5 16.4 + - - +
347A GLN 3.4 0.5 - - - -
348A ASN* 1.3 90.4 - - + +
350A LEU* 1.3 65.9 + - - +
351A GLN* 4.6 5.4 - - + +
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Residues in contact with LEU 350 (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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283A ASP* 3.2 8.1 - - - +
284A LEU* 2.9 50.3 + - + +
287A LEU* 3.7 16.6 - - + -
294A VAL* 3.8 34.5 - - + -
296A VAL* 5.2 0.2 - - + -
322A MET* 3.6 35.0 - - + -
341A LEU* 3.7 17.3 - - + -
342A VAL 3.7 5.8 - - - +
343A GLU* 4.7 0.9 - - - +
349A VAL* 1.3 74.7 - - - +
351A GLN* 1.3 83.9 + - - +
352A VAL* 5.3 2.7 - - + -
367A LEU* 5.1 4.7 - - + -
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Residues in contact with GLN 351 (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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280A ILE* 3.0 34.4 - - + +
282A ALA 3.7 4.7 - - - +
283A ASP* 4.7 7.7 - - + +
340A ARG 3.6 0.5 - - - +
341A LEU* 3.2 8.1 - - - +
342A VAL* 2.7 44.6 + - + +
343A GLU 4.6 0.2 - - - +
344A GLY* 3.7 24.7 - - - -
345A GLN 5.5 0.6 - - - +
349A VAL* 4.6 5.8 - - + +
350A LEU* 1.3 81.9 - - - +
352A VAL* 1.3 64.5 + - - +
353A ARG* 3.2 35.7 + - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.4 4.9 - - - -
281A LEU* 2.8 51.3 + - + -
282A ALA* 3.0 30.2 + - + +
283A ASP* 5.6 0.7 - - - -
296A VAL* 4.2 28.7 - - + -
339A ILE* 4.3 14.6 - - + -
340A ARG 3.6 3.1 - - - -
341A LEU* 3.6 19.5 - - + -
350A LEU* 5.3 4.3 - - + -
351A GLN* 1.3 74.0 - - - +
353A ARG* 1.3 60.6 + - - +
365A VAL* 5.5 5.2 - - + -
367A LEU* 5.3 7.4 - - + -
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Residues in contact with ARG 353 (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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277A ASP* 5.2 1.2 + - - -
278A HIS* 3.4 52.7 + - + -
279A LEU 3.2 7.9 - - - +
280A ILE* 4.4 8.0 - - + +
281A LEU* 4.9 0.4 - - - -
339A ILE* 3.1 25.5 - - - +
340A ARG* 2.9 38.6 + - + +
342A VAL* 3.1 38.4 - - + +
343A GLU 5.2 2.2 + - - -
351A GLN* 3.2 20.7 + - + -
352A VAL* 1.3 78.6 - - - +
354A VAL* 1.3 67.9 + - - +
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Residues in contact with VAL 354 (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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278A HIS* 3.5 5.3 - - - -
279A LEU* 2.9 40.6 + - + +
281A LEU* 3.8 19.7 - - + -
338A PRO* 3.1 26.5 - - + +
339A ILE* 4.2 10.3 - - + +
340A ARG* 5.6 2.5 - - - +
353A ARG* 1.3 80.2 - - - +
355A ALA* 1.3 66.8 + - - +
358A SER* 3.3 23.1 - - - -
359A MET* 3.8 21.5 - - - -
362A LEU* 5.1 3.4 - - + -
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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