Contacts of the strand formed by residues 140 - 147 (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 GLN 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ARG* 2.7 25.0 + - - +
135B GLY 4.0 1.0 - - - +
136B MET* 3.5 11.7 - - + +
137B GLN* 2.8 43.2 + - - +
138B LYS 3.2 15.6 - - - +
139B ASP* 1.3 80.0 - - - +
141B SER* 1.3 61.9 + - - +
301B ILE* 3.3 24.6 - - + +
302B VAL 3.0 12.1 - - - +
303B ASP* 2.8 30.4 + - - +
304B ASP* 3.5 6.1 - - - +
310B ALA* 3.7 7.7 - - - +
707B CL 3.7 20.0 - - - +
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Residues in contact with SER 141 (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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141A SER* 5.3 4.6 + - - -
143A HIS* 4.9 1.4 + - - -
65B ARG* 3.7 12.3 - - - +
136B MET* 4.2 1.1 - - - -
140B GLN* 1.3 75.5 - - - +
142B ILE* 1.3 70.2 + - - +
143B HIS* 3.2 27.8 + - - -
301B ILE* 3.6 0.9 - - - +
302B VAL* 2.9 31.9 + - - +
304B ASP* 3.7 10.7 + - - -
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Residues in contact with ILE 142 (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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305A ASN* 4.8 5.4 + - - +
307A ASN* 3.2 18.0 + - - -
65B ARG* 5.0 0.6 - - - +
69B ILE* 4.3 16.4 - - + -
72B SER* 5.9 2.7 - - - +
73B LEU* 4.4 17.9 - - + -
133B ILE* 4.2 20.2 - - + -
136B MET* 4.0 25.8 - - + -
141B SER* 1.3 83.6 + - - +
143B HIS* 1.3 66.1 + - - +
144B ILE* 4.9 3.1 - - + -
299B VAL* 3.9 22.4 - - + -
300B THR 3.3 7.0 - - - +
301B ILE* 3.7 28.3 - - + -
313B LEU* 4.7 2.5 - - + -
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Residues in contact with HIS 143 (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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141A SER* 5.1 0.2 + - - -
143A HIS* 3.1 34.3 + + - -
307A ASN* 3.4 2.9 - - - +
141B SER* 3.2 26.1 + - - -
142B ILE* 1.3 76.6 - - - +
144B ILE* 1.3 62.3 + - - +
145B GLU* 3.1 16.0 + - - +
298B ARG 3.6 0.3 - - - +
299B VAL* 3.2 6.1 - - - +
300B THR* 2.8 44.5 + - - +
302B VAL* 3.4 24.8 - - + +
307B ASN* 3.4 23.1 - - - -
701B CD 2.2 28.3 - - - -
706B CL 3.9 1.1 - - + -
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASN 4.0 6.7 - - - +
306A SER 4.9 2.7 - - - +
307A ASN* 3.0 44.2 + - + +
72B SER* 3.8 24.5 - - - +
73B LEU* 4.3 10.5 - - + -
105B TYR* 3.5 44.4 - - + +
142B ILE* 4.8 3.8 - - + +
143B HIS* 1.3 78.0 - - - +
145B GLU* 1.3 68.0 + - - +
146B ASN 4.1 0.5 + - - -
297B TYR* 5.6 2.5 - - + -
298B ARG 3.2 7.9 - - - +
299B VAL* 4.3 11.2 - - + -
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Residues in contact with GLU 145 (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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143A HIS* 4.1 0.2 - - - -
145A GLU* 3.1 10.3 - - + +
307A ASN* 5.0 0.2 - - - -
1001A CD 2.4 27.5 - - - -
1005A CL 3.7 5.7 - - - +
143B HIS* 3.1 13.2 + - + +
144B ILE* 1.3 80.9 - - - +
146B ASN* 1.3 67.1 + - - +
147B LEU* 4.1 2.3 - - + +
297B TYR* 3.3 4.2 - - - +
298B ARG* 2.7 62.9 + - - +
300B THR* 5.0 0.7 - - - +
701B CD 2.1 27.2 - - - -
706B CL 3.5 19.5 - - + -
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Residues in contact with ASN 146 (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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298A ARG* 5.2 8.2 + - - +
144B ILE 4.1 1.4 + - - -
145B GLU* 1.3 76.2 + - - +
147B LEU* 1.3 66.4 + - - +
148B LYS* 3.6 24.0 + - - +
295B ASP* 3.4 29.8 + - - +
296B GLY 3.4 12.8 - - - +
297B TYR* 4.4 4.4 - - - +
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Residues in contact with LEU 147 (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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145B GLU* 4.1 3.4 - - + +
146B ASN* 1.3 80.2 - - - +
148B LYS* 1.3 66.6 + - - +
295B ASP* 3.5 2.4 - - - -
296B GLY* 2.6 43.7 + - - +
297B TYR* 3.4 29.6 - - - +
298B ARG* 4.2 32.5 - - + +
315B GLU* 4.7 11.2 - - + -
316B LYS 3.8 11.0 - - - +
317B LYS* 4.8 4.7 - - - -
318B LYS* 3.7 13.0 - - + +
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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