Contacts of the strand formed by residues 370 - 376 (chain B) in PDB entry 1K7E
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 370 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B ARG 3.2 7.6 + - - +
71B THR* 3.5 25.0 + - - +
72B THR* 2.8 27.0 + - - +
222B ARG* 4.9 1.1 - - - -
225B ASP* 3.1 11.8 - - + +
361B MET* 3.2 41.4 + - - +
362B MET* 3.9 1.2 - - - +
365B GLN 4.1 1.8 + - - -
368B LYS* 3.8 40.9 + - + +
369B GLU* 1.3 78.6 - - - +
371B LEU* 1.3 61.8 + - - +
372B LEU* 3.9 26.7 - - + +
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Residues in contact with LEU 371 (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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72B THR* 3.6 23.1 - - + +
74B TYR* 4.0 28.0 - - + -
216B ILE* 4.2 8.3 - - + -
220B GLU* 4.0 28.9 - - + +
222B ARG* 3.7 29.8 - - + +
223B LEU 3.8 20.6 - - - +
224B PRO* 3.7 11.5 - - + +
225B ASP* 2.6 31.4 + - - +
226B ALA 3.6 1.2 + - - -
370B GLN* 1.3 71.4 - - - +
372B LEU* 1.3 64.5 + - - +
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Residues in contact with LEU 372 (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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71B THR* 4.1 21.1 - - + -
72B THR 3.0 11.4 + - - +
73B LEU* 3.3 15.1 - - + -
74B TYR* 2.9 27.3 + - - +
225B ASP* 4.7 2.5 - - + -
226B ALA* 3.5 17.9 - - + +
228B ILE* 4.4 7.2 - - + -
358B ALA* 4.2 17.9 - - + +
361B MET* 4.1 40.2 - - + -
370B GLN* 3.9 24.0 - - + +
371B LEU* 1.3 82.6 - - - +
373B VAL* 1.3 65.3 + - - +
374B VAL 4.2 0.2 - - - -
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Residues in contact with VAL 373 (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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59B LEU* 4.3 10.5 - - + -
74B TYR* 3.3 13.5 - - + +
76B LYS* 4.4 4.9 - - + +
212B THR* 3.8 27.8 - - + -
216B ILE* 4.2 16.4 - - + -
224B PRO* 3.9 24.7 - - + -
226B ALA 3.0 6.5 + - - +
227B VAL* 3.3 14.9 - - + +
228B ILE* 2.8 34.0 + - - +
240B MET* 4.6 5.8 - - - +
371B LEU* 5.7 0.2 - - + -
372B LEU* 1.3 78.8 - - - +
374B VAL* 1.3 70.0 + - - +
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Residues in contact with VAL 374 (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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73B LEU* 3.7 9.6 - - + +
74B TYR 2.8 10.7 + - - +
75B LEU* 3.3 19.1 - - + -
76B LYS 3.0 23.2 + - - -
228B ILE* 3.6 11.9 - - + -
351B SER 5.0 0.4 - - - +
354B ALA* 4.0 18.8 - - + +
355B LEU* 4.0 17.9 - - + +
358B ALA* 3.6 31.2 - - + -
372B LEU 4.2 0.2 - - - -
373B VAL* 1.3 79.0 - - - +
375B ASN* 1.3 76.4 + - - +
376B LEU* 4.1 8.3 - - + +
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Residues in contact with ASN 375 (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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76B LYS* 3.5 28.7 - - - +
78B GLU* 3.6 15.5 - - - +
208B ILE* 3.8 16.0 - - - +
228B ILE 3.0 15.4 + - - +
229B ALA* 4.1 4.5 - - + -
230B CYS 5.2 0.5 + - - -
236B ASN* 3.0 48.4 + - - +
240B MET* 3.9 13.0 - - + +
351B SER* 4.3 5.5 - - - -
354B ALA* 4.4 6.9 - - - +
373B VAL* 4.1 1.2 + - - +
374B VAL* 1.3 77.7 - - - +
376B LEU* 1.4 63.9 + - - +
377B SER* 3.0 11.7 + - - -
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Residues in contact with LEU 376 (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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75B LEU* 4.2 22.7 - - + -
76B LYS 2.8 18.8 + - - +
77B ARG* 4.1 4.7 - - - +
78B GLU* 3.2 8.1 + - - -
79B ASP* 3.1 45.9 + - + +
339B LEU* 4.1 14.6 - - + -
345B ILE* 3.9 20.6 - - + -
347B PRO* 3.6 24.7 - - + -
351B SER* 3.9 11.9 - - - +
355B LEU* 5.5 3.6 - - + -
374B VAL* 3.4 8.7 + - + -
375B ASN* 1.4 68.4 - - - +
377B SER* 1.3 64.5 + - - +
378B GLY 3.0 14.4 + - - +
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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