Contacts of the strand formed by residues 140 - 147 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 2.7 32.6 + - - +
135A GLY 4.2 1.9 - - - +
136A MET* 3.6 7.9 - - + +
137A GLN* 2.9 41.0 + - - +
138A LYS 3.2 14.7 - - - +
139A ASP* 1.3 80.3 - - - +
141A SER* 1.3 55.7 + - - +
301A ILE* 3.1 23.9 - - + +
302A VAL 3.1 12.3 - - - +
303A ASP* 2.6 32.0 + - - +
304A ASP* 3.3 8.3 + - - +
310A ALA* 3.7 18.0 - - - +
1006A CL 3.9 8.9 - - - +
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Residues in contact with SER 141 (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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65A ARG* 3.7 13.0 - - - +
136A MET* 5.6 0.7 - - - -
140A GLN* 1.3 76.6 - - - +
142A ILE* 1.3 67.1 + - - +
143A HIS* 3.2 25.4 + - - -
301A ILE* 3.7 2.8 - - - -
302A VAL* 3.0 32.1 + - - -
304A ASP* 3.7 11.5 + - - -
141B SER* 5.3 2.9 + - - -
143B HIS* 5.1 0.7 + - - -
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 5.1 0.2 - - - +
69A ILE* 3.9 25.8 - - + -
72A SER* 5.8 2.9 - - - +
73A LEU* 4.2 19.1 - - + -
133A ILE* 4.3 9.0 - - + -
136A MET* 3.1 36.3 - - + -
141A SER* 1.3 76.3 + - - +
143A HIS* 1.3 65.3 + - - +
144A ILE* 4.9 2.0 - - + -
299A VAL* 4.0 22.2 - - + -
300A THR 3.4 7.2 - - - +
301A ILE* 3.8 23.6 - - + -
313A LEU* 4.6 2.2 - - + -
305B ASN* 5.3 3.8 + - - -
307B ASN* 3.3 17.3 + - - -
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Residues in contact with HIS 143 (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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141A SER* 3.2 27.0 + - - -
142A ILE* 1.3 76.7 - - - +
144A ILE* 1.3 64.0 + - - +
145A GLU* 3.2 12.7 + - - +
298A ARG 3.6 0.6 - - - +
299A VAL* 3.3 6.4 - - - +
300A THR* 2.9 45.9 + - - +
302A VAL* 3.5 25.9 - - + +
307A ASN* 3.5 17.0 - - - -
1001A CD 2.4 28.2 - - - -
1005A CL 4.1 0.4 - - + -
141B SER* 4.9 0.8 + - - -
143B HIS* 3.1 40.2 + + - -
307B ASN* 3.6 2.7 - - - -
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Residues in contact with ILE 144 (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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72A SER* 4.1 15.5 - - - +
73A LEU* 3.9 22.2 - - + -
105A TYR* 3.6 52.9 - - + +
142A ILE* 4.8 3.1 - - + +
143A HIS* 1.3 79.4 - - - +
145A GLU* 1.3 71.3 + - - +
146A ASN 4.2 0.3 + - - -
297A TYR* 5.5 2.7 - - + -
298A ARG 3.3 6.7 - - - +
299A VAL* 4.5 5.6 - - + -
305B ASN 4.5 3.1 - - - +
306B SER 5.5 1.8 - - - +
307B ASN* 3.0 40.7 + - + +
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Residues in contact with GLU 145 (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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143A HIS* 3.2 13.1 + - + +
144A ILE* 1.3 82.3 - - - +
146A ASN* 1.3 63.4 + - - +
147A LEU* 4.4 1.9 - - + +
297A TYR* 3.1 8.3 - - - +
298A ARG* 2.8 57.9 + - + +
300A THR* 5.2 0.7 - - - +
1001A CD 2.2 29.5 - - - -
1005A CL 3.6 14.1 - - + -
143B HIS* 4.0 0.3 - - - -
145B GLU* 3.0 16.0 - - + +
298B ARG* 4.2 5.3 + - - +
701B CD 2.3 29.3 - - - -
706B CL 3.6 6.1 - - - +
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Residues in contact with ASN 146 (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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144A ILE 4.2 0.8 + - - -
145A GLU* 1.3 77.0 + - - +
147A LEU* 1.3 64.3 + - - +
148A LYS* 3.4 26.2 + - - +
295A ASP* 3.6 32.3 + - - +
296A GLY 3.7 6.0 + - - -
297A TYR* 4.4 3.0 - - - +
298B ARG* 5.4 8.4 + - - +
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Residues in contact with LEU 147 (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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145A GLU* 4.9 3.8 - - + +
146A ASN* 1.3 79.0 - - - +
148A LYS* 1.3 67.2 + - - +
295A ASP* 3.4 1.9 - - - -
296A GLY* 2.7 42.9 + - - -
297A TYR* 3.6 30.1 - - - +
298A ARG* 3.8 31.9 - - + +
315A GLU* 4.4 16.2 - - + +
316A LYS 3.7 13.2 - - - +
317A LYS* 4.9 1.6 - - - -
318A LYS* 3.4 18.0 - - + +
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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