Contacts of the strand formed by residues 311 - 318 (chain A) in PDB entry 1H7B
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 ASN 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A THR* 3.9 4.3 - - - -
78A ASN* 3.0 45.2 + - - +
79A CYS* 3.2 27.6 + - - +
288A MET* 4.0 2.9 - - + -
292A SER* 4.1 4.1 + - - -
310A ASN* 1.3 77.1 - - - +
312A LEU* 1.3 64.3 + - - +
313A GLY 2.7 36.8 + - - +
396A SER* 3.0 29.5 + - - +
398A SER* 2.9 24.1 + - - -
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Residues in contact with LEU 312 (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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76A PHE 5.2 1.6 - - - +
77A THR* 4.5 9.3 - - + -
78A ASN* 4.3 3.0 + - - +
124A TYR* 3.8 8.6 + - - -
310A ASN* 3.3 24.9 - - - +
311A ASN* 1.3 73.9 - - - +
313A GLY* 1.3 56.8 + - - +
355A ARG* 5.0 10.7 - - - +
356A ILE* 4.1 17.3 - - + +
359A LEU* 4.3 12.4 - - + +
390A PHE* 3.7 30.5 - - + -
395A SER* 3.3 18.2 - - - +
396A SER 2.8 11.9 + - - +
397A VAL* 3.8 25.4 - - + -
436A PHE* 3.9 24.7 - - + -
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Residues in contact with GLY 313 (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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78A ASN* 3.8 3.3 - - - +
124A TYR* 3.5 16.2 - - - -
311A ASN* 2.7 19.8 + - - +
312A LEU* 1.3 75.7 - - - +
314A VAL* 1.3 64.8 + - - -
352A LEU* 4.6 5.8 - - - -
355A ARG* 4.5 7.2 - - - -
396A SER 4.8 0.2 + - - -
397A VAL* 4.2 2.7 - - - +
398A SER* 2.9 27.4 + - - +
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Residues in contact with VAL 314 (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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66A HIS* 3.2 58.6 + - + +
67A ASP* 5.3 3.0 + - - +
78A ASN* 3.9 18.4 - - - +
124A TYR* 4.8 0.6 + - - -
313A GLY* 1.3 80.1 - - - +
315A VAL* 1.3 72.6 + - - +
316A THR* 3.7 9.2 - - - +
352A LEU* 4.3 0.4 - - - -
355A ARG* 3.7 7.8 + - - +
398A SER* 3.4 18.2 - - - +
400A GLY 4.3 1.3 - - - +
441A TYR* 3.8 32.8 - - + -
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Residues in contact with VAL 315 (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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63A ILE* 4.3 10.5 - - + -
64A HIS 3.3 8.7 - - - +
65A VAL* 4.3 16.8 - - + -
314A VAL* 1.3 78.5 - - - +
316A THR* 1.3 61.6 + - - +
348A CYS* 4.2 23.3 - - + +
351A ALA* 3.9 30.1 - - + +
352A LEU* 3.4 33.0 - - + +
355A ARG* 4.6 4.0 - - - -
398A SER 3.1 5.3 + - - -
399A LEU* 3.5 8.3 - - - +
400A GLY 2.7 26.2 + - - +
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Residues in contact with THR 316 (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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63A ILE* 3.1 8.9 - - - +
64A HIS* 2.8 36.4 + - - -
66A HIS* 2.6 29.0 + - - -
314A VAL* 3.7 3.3 - - - +
315A VAL* 1.3 73.7 - - - +
317A LEU* 1.3 73.0 + - - +
348A CYS* 5.0 0.2 - - - -
400A GLY 3.5 2.7 - - - -
401A TYR* 3.6 20.0 - - - +
402A ILE* 4.2 2.2 - - + -
443A THR* 2.8 22.1 + - - +
448A LEU* 3.8 12.3 - - + -
452A PHE* 3.8 16.6 - - + -
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Residues in contact with LEU 317 (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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62A ILE 3.9 11.0 - - - +
63A ILE* 4.7 0.9 - - + -
315A VAL 4.1 0.2 + - - -
316A THR* 1.3 75.7 - - - +
318A ASN* 1.3 73.0 + - - +
319A LEU* 3.3 30.5 + - + -
322A ILE* 3.7 26.5 - - + -
341A PHE* 4.7 3.4 - - + -
344A ARG* 4.2 18.2 - - + +
345A MET* 4.0 24.7 - - + -
348A CYS* 3.8 24.7 - - - -
399A LEU* 4.8 2.9 - - + -
400A GLY 2.9 16.1 + - - +
401A TYR* 3.4 19.0 - - + +
402A ILE 3.6 3.5 + - - -
423A MET* 4.4 7.0 - - - -
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Residues in contact with ASN 318 (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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61A GLY 2.8 30.0 + - - +
62A ILE 3.3 9.6 + - - +
316A THR 3.9 1.4 + - - -
317A LEU* 1.3 75.2 - - - +
319A LEU* 1.3 62.1 + - - +
320A PRO* 3.3 12.1 - - - +
321A ARG* 3.3 25.0 + - + +
322A ILE* 3.4 17.8 + - - +
344A ARG* 5.3 0.3 + - - -
402A ILE* 4.5 1.1 - - - -
452A PHE* 3.5 36.3 - - + +
456A ASP* 3.1 24.0 + - - -
472A TYR* 3.6 6.8 - - - -
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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