Contacts of the strand formed by residues 137 - 144 (chain B) in PDB entry 1QM4
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 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 4.6 9.1 + - - +
184A GLN* 4.7 2.9 - - - -
135B ASP 3.2 4.4 + - - -
136B GLN* 1.3 75.4 - - - +
138B LEU* 1.3 61.2 + - - +
139B MET* 4.3 15.9 - - - -
291B VAL* 5.4 2.7 - - - -
320B SER* 3.6 3.8 - - - -
321B TYR* 2.9 35.3 + - - +
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Residues in contact with LEU 138 (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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20A MET 4.7 0.9 - - - +
21A PHE* 3.7 14.8 - - + -
22A THR* 3.6 41.9 - - + +
137B GLY* 1.3 72.6 - - - +
139B MET* 1.3 70.3 + - - +
140B PHE* 3.5 34.5 + - + -
279B GLY* 4.9 8.8 + - - -
318B GLN* 3.3 33.2 - - + +
319B VAL 3.5 7.9 - - - +
320B SER* 3.3 21.1 - - - +
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Residues in contact with MET 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLY* 4.3 7.4 - - - -
138B LEU* 1.3 95.5 - - - +
140B PHE* 1.3 64.3 + - - +
291B VAL* 3.7 14.6 - - + +
292B ASP* 3.1 41.1 - - - +
295B ALA* 3.7 29.8 - - + +
296B ALA* 3.7 17.0 - - + +
318B GLN* 3.6 2.9 - - - -
319B VAL* 2.7 47.9 + - + -
321B TYR* 4.4 9.6 - - - -
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Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.5 30.5 - + - -
274A GLY* 3.9 6.7 - - - -
138B LEU* 3.5 19.7 - - + -
139B MET* 1.3 75.6 - - - +
141B GLY* 1.3 60.5 + - - +
272B TYR* 4.6 7.9 + - + -
277B ALA* 3.4 52.3 - - + +
278B HIS* 3.8 2.0 - - - -
279B GLY* 3.9 23.3 - - - -
296B ALA* 4.1 12.4 - - - +
299B ALA* 3.6 10.9 - - - +
316B LEU* 4.1 15.7 - - + -
317B VAL 3.4 2.2 - - - -
318B GLN* 3.5 37.5 - - + -
381B PHE* 6.0 0.7 - - - -
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Residues in contact with GLY 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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140B PHE* 1.3 76.1 - - - +
142B TYR* 1.3 61.7 + - - -
272B TYR* 3.9 6.3 - - - -
299B ALA* 3.5 25.5 - - - +
300B ARG 4.0 0.2 - - - -
303B ALA* 3.9 7.0 - - - -
316B LEU* 3.1 9.6 - - - +
317B VAL* 2.6 32.3 + - - -
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Residues in contact with TYR 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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141B GLY* 1.3 74.2 - - - +
143B ALA* 1.3 55.6 + - - +
144B THR* 3.8 31.1 + - + +
146B GLU* 5.0 0.3 + - - -
150B CYS 5.5 0.2 - - - -
152B PRO* 3.8 15.9 - - + -
196B VAL* 5.0 0.7 - - - +
272B TYR* 3.2 45.7 + + + -
275B TRP* 3.2 29.7 + + - -
276B GLY* 4.0 21.1 - - - -
299B ALA 4.5 0.2 + - - -
300B ARG* 2.7 30.1 + - - -
303B ALA* 3.6 5.6 - - - +
314B ARG* 3.0 34.2 + - + +
315B VAL 3.3 23.1 - - - -
316B LEU* 4.1 8.5 - - + -
336B TYR* 4.1 15.0 - + - -
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Residues in contact with ALA 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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142B TYR* 1.3 82.4 - - - +
144B THR* 1.3 62.4 + - - +
150B CYS* 3.4 11.0 - - + +
300B ARG* 3.5 9.4 - - - +
303B ALA* 3.5 32.8 - - + +
304B LYS* 3.7 4.7 - - - +
307B VAL* 3.6 12.3 - - + -
314B ARG* 3.3 4.3 - - - +
315B VAL* 2.8 32.3 + - + +
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Residues in contact with THR 144 (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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142B TYR* 3.8 25.0 + - + +
143B ALA* 1.3 78.3 - - - +
145B ASP* 1.3 63.7 + - - +
146B GLU* 2.7 33.3 + - - +
147B THR 4.0 0.5 + - - +
150B CYS* 3.0 26.1 + - - +
151B MET* 3.5 6.1 + - - +
152B PRO* 3.5 25.8 - - + -
196B VAL* 4.7 5.5 + - - +
307B VAL* 4.4 4.5 - - - +
313B ARG 3.6 9.1 + - - -
314B ARG* 4.2 7.2 - - - +
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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