Contacts of the strand formed by residues 296 - 303 (chain B) in PDB entry 1MWT
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 GLY 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ASN* 3.4 10.7 - - - +
147B LEU* 2.6 39.5 + - - -
294B GLU 3.6 1.4 + - - -
295B ASP* 1.3 74.1 - - - +
297B TYR* 1.3 58.3 + - - +
316B LYS* 3.2 20.0 - - - -
317B LYS 4.1 2.7 - - - -
318B LYS* 3.8 12.5 - - - +
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Residues in contact with TYR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ASN 4.9 2.0 + - - -
105B TYR* 2.6 67.5 + + + -
144B ILE* 5.6 2.9 - - + -
145B GLU 3.3 12.1 - - - +
146B ASN* 4.6 4.3 - - - +
147B LEU* 3.4 8.0 - - - +
295B ASP 5.7 0.9 - - - -
296B GLY* 1.3 75.7 - - - +
298B ARG* 1.3 72.4 + - - +
299B VAL* 5.0 0.4 - - + -
314B ILE* 4.1 12.3 - - + +
315B GLU* 3.8 1.0 - - - -
316B LYS* 3.0 67.4 + - + +
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLU* 4.2 6.3 + - - +
146A ASN* 5.4 9.1 + - - +
143B HIS 3.6 0.3 - - - +
144B ILE* 3.2 5.2 - - - +
145B GLU* 2.7 59.1 + - + +
147B LEU* 4.2 22.7 - - + +
297B TYR* 1.3 79.8 - - - +
299B VAL* 1.3 65.5 + - - +
300B THR* 3.7 25.4 - - + +
309B ILE* 4.3 15.4 - - - +
312B THR* 4.3 4.5 - - + -
314B ILE 3.5 10.1 - - - +
315B GLU* 3.5 26.6 + - - +
706B CL 3.5 20.8 - - - +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.9 25.6 - - + -
105B TYR* 4.0 37.7 - - + -
108B ILE* 5.3 0.7 - - + -
142B ILE* 3.9 13.2 - - + -
143B HIS 3.2 7.4 - - - +
144B ILE* 4.3 8.3 - - + -
297B TYR* 5.0 1.6 - - + -
298B ARG* 1.3 77.9 - - - +
300B THR* 1.3 65.1 - - - +
312B THR 3.9 0.2 - - - -
313B LEU* 3.0 38.9 + - + -
314B ILE* 2.9 28.0 + - + +
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ILE* 3.3 10.8 - - - +
143B HIS* 2.8 36.1 + - - +
145B GLU* 5.0 0.7 - - - +
298B ARG* 3.7 29.6 - - + +
299B VAL* 1.3 79.6 - - - +
301B ILE* 1.3 66.0 + - - +
302B VAL* 3.5 2.3 - - - +
309B ILE* 4.0 15.9 - - + -
311B HIS 3.2 14.8 - - - +
312B THR* 3.8 14.1 - - - +
313B LEU* 4.3 2.5 - - - +
706B CL 3.2 22.5 - - - +
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 4.1 8.5 - - + -
134B PRO 3.7 22.4 - - - +
136B MET* 3.8 20.0 - - + +
140B GLN* 3.3 37.0 - - + +
141B SER 3.6 5.6 - - - +
142B ILE* 3.7 17.3 - - + -
300B THR* 1.3 71.7 - - - +
302B VAL* 1.3 64.5 + - - +
309B ILE* 3.8 1.2 - - - -
310B ALA* 2.9 28.2 + - + -
311B HIS* 2.9 29.3 + - + +
313B LEU* 3.8 24.5 - - + -
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLN* 3.0 9.5 - - - -
141B SER* 2.9 36.7 + - - +
143B HIS* 3.4 46.9 - - + +
300B THR* 3.5 14.4 - - - +
301B ILE* 1.3 79.0 - - - +
303B ASP* 1.3 77.7 + - - +
304B ASP* 4.2 0.3 - - - +
307B ASN* 3.3 27.6 - - - +
308B THR 3.3 10.5 - - - +
309B ILE* 4.8 3.8 - - + -
706B CL 3.9 6.3 - - + -
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Residues in contact with ASP 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TRP* 5.7 4.0 - - - +
137B GLN* 5.2 1.0 - - - +
138B LYS 5.3 0.3 - - - +
139B ASP* 3.8 5.0 - - - +
140B GLN* 2.8 29.2 + - - +
302B VAL* 1.3 89.2 - - - +
304B ASP* 1.3 67.2 + - - +
305B ASN 3.5 0.3 + - - -
306B SER* 3.4 17.5 - - - +
307B ASN* 3.3 8.8 + - - -
308B THR* 2.9 22.8 + - - +
310B ALA* 4.0 11.7 + - - +
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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