Contacts of the strand formed by residues 200 - 205 (chain A) in PDB entry 5MLG
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 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A PHE* 3.4 12.9 - - - -
198A GLU* 3.1 28.7 + - + +
199A GLU* 1.3 83.0 - - - +
201A PHE* 1.3 62.9 + - - +
219A GLY 2.8 24.4 + - - -
220A GLY* 3.4 34.1 - - - +
367A GLU* 3.8 21.1 - - + +
368A PHE 3.2 11.4 - - - +
369A ASP* 3.6 28.9 - - - +
371A HIS* 6.1 0.2 - - + -
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Residues in contact with PHE 201 (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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82A THR* 3.8 14.8 - - + -
173A MET* 3.6 55.4 - - + -
187A PHE* 3.8 26.7 - + + -
200A VAL* 1.3 76.5 - - - +
202A SER* 1.3 57.1 + - - +
203A VAL* 4.2 11.4 - - + -
216A VAL* 4.6 4.3 - - + -
217A VAL 3.1 15.3 - - - +
218A LEU* 3.9 16.8 - - + -
220A GLY 4.3 1.1 - - - -
241A TRP* 4.1 10.8 - + - -
367A GLU* 4.5 1.8 - - - -
368A PHE* 2.7 74.0 + + + +
370A ARG* 5.0 0.2 - - + -
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Residues in contact with SER 202 (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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201A PHE* 1.3 73.5 - - - +
203A VAL* 1.3 63.2 + - - +
215A GLU 3.9 0.5 - - - +
216A VAL* 3.4 5.4 - - - +
217A VAL* 2.9 33.9 + - - +
220A GLY 2.7 23.0 + - - -
221A SER* 3.4 12.1 - - - -
365A TYR* 2.7 32.2 + - - -
366A THR 3.2 14.6 - - - -
367A GLU* 3.9 6.5 - - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.5 0.7 - - + -
80A PHE* 6.4 1.3 - - + -
82A THR* 5.4 0.2 - - + -
201A PHE* 4.2 12.3 - - + -
202A SER* 1.3 79.5 - - - +
204A TYR* 1.3 60.6 + - - +
205A TYR* 3.7 38.1 - - + +
215A GLU 3.6 2.7 - - - +
216A VAL* 4.2 21.8 - - + +
267A THR* 3.8 15.0 - - + -
361A ILE* 3.4 21.0 - - + +
365A TYR* 3.3 13.5 - - - -
366A THR 3.0 10.2 + - - +
368A PHE* 3.7 26.5 - - + -
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Residues in contact with TYR 204 (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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13A LEU* 4.1 1.4 - - - +
203A VAL* 1.3 72.3 - - - +
205A TYR* 1.3 76.6 + - - +
206A SER* 3.2 35.2 - - - -
207A ARG 4.8 0.2 + - - -
214A GLY* 3.2 12.9 - - - -
215A GLU* 2.8 49.6 + - + +
225A HIS* 3.3 51.8 + + + -
361A ILE 5.4 1.1 - - - -
365A TYR* 3.5 20.1 - + + -
380A ALA* 4.3 17.7 - - + -
381A ARG 3.3 24.4 + - - -
382A ALA* 3.9 12.1 - - - +
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Residues in contact with TYR 205 (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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13A LEU* 3.7 19.3 - - + +
63A TYR* 3.4 49.1 - + + -
80A PHE 4.8 1.0 + - - -
203A VAL* 3.7 11.6 - - + +
204A TYR* 1.3 88.3 - - - +
206A SER* 1.3 64.2 + - - +
213A GLY 4.0 3.8 - - - -
267A THR* 3.3 37.3 + - - +
358A ALA* 3.5 33.9 - - + -
361A ILE* 3.7 31.7 + - + -
362A ARG* 3.6 34.6 - - + +
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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