Contacts of the strand formed by residues 381 - 388 (chain B) in PDB entry 1QMB
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 SER 381 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A THR* 3.9 7.2 - - - -
30A LEU* 4.3 11.9 - - - -
55A VAL* 4.3 4.1 - - - +
99A LEU* 3.7 20.0 - - - +
103A LEU* 3.9 2.3 - - - +
375B ILE* 3.2 4.6 - - - -
376B GLU 3.1 22.8 + - - -
379B THR* 2.9 25.1 + - - -
380B LYS* 1.3 79.5 - - - +
382B PRO* 1.3 69.6 - - - +
383B LEU* 3.2 18.4 + - - +
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Residues in contact with PRO 382 (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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27A THR 4.7 2.0 - - - +
30A LEU* 4.2 9.4 - - + -
31A ALA* 4.0 34.8 - - + +
34A ALA* 4.1 12.8 - - + -
35A PHE* 6.3 0.7 - - + -
54A PRO* 3.5 25.9 - - + +
55A VAL* 3.3 13.1 - - + +
373B LEU* 4.7 17.7 - - + -
374B MET 3.4 8.3 - - - +
375B ILE* 4.7 3.6 - - + -
380B LYS 4.4 1.3 - - - +
381B SER* 1.3 83.8 - - - +
383B LEU* 1.3 67.4 + - - +
384B PHE 3.3 4.3 - - - +
385B MET* 5.7 0.7 - - + -
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Residues in contact with LEU 383 (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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53A SER* 3.0 28.8 + - - -
54A PRO 3.8 0.2 - - - -
55A VAL* 3.9 10.6 + - + -
103A LEU* 3.8 10.5 - - + -
112A LEU* 3.7 37.2 - - + -
188A ILE* 4.3 9.0 - - + +
190A PHE* 3.8 20.9 - - + -
248A ALA* 5.4 1.1 - - + -
374B MET* 2.6 15.8 + - + +
375B ILE 4.8 2.2 - - - -
376B GLU* 3.5 27.8 - - + +
381B SER* 3.5 23.6 - - - +
382B PRO* 1.3 75.1 - - - +
384B PHE* 1.3 75.5 + - + +
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Residues in contact with PHE 384 (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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51A PHE* 3.5 24.2 - + + -
52A PHE 3.4 7.6 - - - -
53A SER* 3.6 22.0 - - - -
54A PRO* 3.8 4.0 - - - -
188A ILE* 3.8 25.4 - - + -
190A PHE* 3.8 19.3 - + + -
336A ALA* 4.9 0.4 - - + -
347A ALA* 3.7 30.5 - - + -
348A ALA 3.9 19.1 - - - -
349A GLY* 4.0 0.7 - - - -
372B PHE* 5.7 0.2 - - - -
373B LEU* 3.1 6.3 - - - +
374B MET* 2.7 63.5 + - + +
382B PRO* 4.5 2.1 - - - +
383B LEU* 1.3 94.4 + - + +
385B MET* 1.3 61.2 + - - +
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Residues in contact with MET 385 (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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34A ALA* 4.2 7.9 - - + +
35A PHE* 3.7 37.9 - - + -
38A TYR* 3.7 43.7 - - + -
51A PHE* 3.4 7.1 - - - -
52A PHE* 3.0 47.8 + - + -
54A PRO* 4.5 5.8 - - + -
267A LEU* 4.1 15.5 - - + -
371B VAL* 4.1 12.3 - - + -
372B PHE* 3.2 14.6 - - - +
373B LEU* 3.8 13.7 - - + +
382B PRO* 5.7 0.7 - - + -
384B PHE* 1.3 77.2 - - - +
386B GLY* 1.3 63.6 + - - +
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Residues in contact with GLY 386 (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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38A TYR* 4.2 5.2 - - - -
50A ILE* 2.8 22.2 - - - -
51A PHE* 4.1 0.2 - - - -
371B VAL* 3.4 7.3 - - - +
372B PHE* 2.7 48.4 + - - +
385B MET* 1.3 79.5 - - - +
387B LYS* 1.3 59.7 + - - -
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Residues in contact with LYS 387 (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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38A TYR* 3.4 15.5 - - + +
42A ALA* 4.5 14.1 + - - +
45A SER* 5.6 2.6 + - - -
47A SER* 5.0 5.4 + - - +
48A THR 4.2 8.2 - - - +
49A ASN* 3.2 7.4 - - - +
50A ILE* 2.7 49.2 + - + +
260A LEU* 4.2 23.1 - - + +
264A GLU* 3.3 29.8 + - - +
293A ILE* 4.9 0.6 - - - +
369B PRO* 5.2 0.7 - - + -
370B PHE 3.4 16.2 - - - +
371B VAL* 4.6 2.0 - - + -
372B PHE* 4.6 0.4 - - - -
386B GLY* 1.3 74.5 - - - +
388B VAL* 1.3 67.5 + - - +
389B VAL* 3.4 29.1 - - + +
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Residues in contact with VAL 388 (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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49A ASN* 3.5 11.0 - - - +
208A PHE* 4.1 4.0 - - + -
291A LEU* 3.3 46.2 - - + -
293A ILE* 4.3 7.4 - - + -
369B PRO* 3.2 23.6 - - - +
370B PHE* 3.0 40.3 + - + -
372B PHE* 3.9 12.6 - - + -
387B LYS* 1.3 72.8 - - - +
389B VAL* 1.3 61.3 + - - +
391B PRO* 4.0 22.0 - - + -
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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