Contacts of the strand formed by residues 244 - 248 (chain A) in PDB entry 1M7X
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 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A PRO 4.1 0.2 - - - -
243A ILE* 1.3 72.5 - - - +
245A ILE* 1.3 61.4 + - - +
280A GLY 4.7 1.8 - - - -
281A PHE* 3.5 15.6 - - - +
282A THR* 2.7 44.4 + - - -
283A HIS 3.1 5.2 + - - -
558A TRP* 3.6 12.9 + - - -
564A LYS* 3.4 6.9 - - - +
607A ASN* 2.6 29.3 + - - -
610A TYR* 4.1 16.2 - - - -
611A ARG* 5.7 0.2 - - - -
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Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ILE* 3.9 18.8 - - + -
244A SER* 1.3 76.8 + - - +
246A TYR* 1.3 62.6 + - - +
281A PHE* 3.7 7.7 - - - -
283A HIS* 3.6 21.8 - - + +
285A GLU* 3.4 40.2 - - + +
333A ILE* 3.8 16.4 - - + -
456A MET* 4.5 13.5 - - - -
481A TRP* 5.9 0.2 - - - +
520A VAL* 4.5 9.4 - - + -
564A LYS 2.7 20.6 + - - +
565A LEU* 4.0 22.4 - - + -
566A LEU 2.8 29.3 + - - +
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Residues in contact with TYR 246 (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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245A ILE* 1.3 71.6 - - - +
247A GLU* 1.3 61.7 + - - +
248A VAL* 3.2 29.4 + - + -
253A TRP* 3.0 19.8 + - - -
272A LEU* 3.7 15.7 - - + -
275A TYR* 3.4 11.2 - + - -
276A ALA* 4.4 7.6 - - + -
281A PHE* 3.5 42.3 - + + -
283A HIS 3.0 13.2 + - - +
284A LEU* 3.7 19.4 - - + +
285A GLU 3.0 21.2 + - - +
566A LEU* 3.5 8.5 - - + -
567A PHE 4.6 0.4 - - - -
568A MET* 3.3 26.7 - - + +
569A GLY 4.3 0.2 + - - -
571A GLU* 2.7 35.6 + - + -
586A TRP* 4.2 1.0 - - - -
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Residues in contact with GLU 247 (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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245A ILE 3.7 2.4 + - - -
246A TYR* 1.3 70.5 - - - +
248A VAL* 1.3 64.7 + - - +
285A GLU* 3.3 28.6 - - + +
287A LEU* 3.7 12.2 - - + +
335A ASP* 4.7 2.1 - - - +
481A TRP* 4.0 8.0 - - - -
524A SER* 3.0 30.9 - - - -
525A HIS* 2.7 40.4 + - - -
565A LEU* 3.8 15.6 - - + +
566A LEU 3.0 7.1 + - - -
567A PHE* 2.9 19.1 - - + +
568A MET 2.9 26.9 + - - -
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TYR* 3.2 42.8 - - + +
247A GLU* 1.3 75.8 - - - +
249A HIS* 1.3 60.1 + - - +
250A LEU* 3.8 13.1 + - + -
253A TRP* 4.3 2.9 - - + -
272A LEU* 4.0 17.7 - - + -
284A LEU* 4.2 4.9 - - + -
285A GLU 2.7 13.5 + - - +
286A LEU* 3.3 30.7 - - + -
287A LEU* 2.9 30.9 + - - +
567A PHE* 4.0 0.9 - - - -
568A MET* 3.7 15.3 - - - -
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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