Contacts of the strand formed by residues 322 - 329 (chain A) in PDB entry 3HI7
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 TRP 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A LEU* 3.4 7.7 - - - +
319A TYR* 2.9 65.3 + + + +
320A GLY 4.3 2.3 - - - +
321A GLY* 1.3 78.4 - - - +
323A SER* 1.3 60.4 + - - +
324A PHE* 4.6 11.7 - + + -
339A VAL* 3.6 25.6 - - + -
340A HIS 3.4 22.2 - - - -
341A PHE* 3.5 21.7 - + + -
346A ILE* 5.2 4.5 - - + -
469A PHE* 3.7 29.1 - + + +
470A TYR 2.8 21.1 + - - -
471A PRO* 5.1 2.0 - - + -
473A GLY* 3.4 31.9 - - - -
474A VAL 3.4 20.9 - - - -
475A MET* 3.7 20.6 - - + -
593A TYR* 4.8 2.2 - + - -
292B PRO* 6.2 0.2 - - - -
293B SER* 4.9 0.3 + - - -
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Residues in contact with SER 323 (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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317A VAL 3.3 6.6 + - - -
318A LEU* 3.5 20.6 - - - +
321A GLY 3.9 0.4 + - - -
322A TRP* 1.3 75.6 - - - +
324A PHE* 1.3 65.1 + - - +
338A ASN 3.5 3.8 + - - +
339A VAL* 4.4 0.2 - - - +
340A HIS* 2.8 49.3 + - - +
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Residues in contact with PHE 324 (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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30A ALA* 5.7 0.2 - - - -
316A ALA* 3.6 3.5 - - - +
317A VAL* 2.8 75.7 + - + +
322A TRP* 4.6 11.9 - + + -
323A SER* 1.3 78.7 + - - +
325A ALA* 1.3 71.9 + - - +
326A PHE* 4.4 2.0 - + - -
336A VAL* 4.0 15.9 - - + -
337A LEU 3.7 11.2 - - - +
338A ASN 3.9 3.8 - - - -
339A VAL* 3.9 16.8 - - + -
418A LEU* 4.8 5.8 - - + -
450A LEU* 4.0 10.3 - - + -
452A LEU* 4.3 11.2 - - + -
469A PHE* 3.5 49.4 - + - -
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Residues in contact with ALA 325 (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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30A ALA* 3.8 16.2 - - + -
33A PHE* 3.7 32.8 - - + -
315A ASN* 3.1 17.0 - - - +
324A PHE* 1.3 81.3 - - - +
326A PHE* 1.3 63.0 + - - +
336A VAL* 3.4 4.5 - - - -
337A LEU* 2.8 33.5 + - + +
338A ASN* 4.6 2.4 + - + +
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Residues in contact with PHE 326 (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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34A SER* 4.8 0.5 - - - -
312A LEU* 3.7 22.9 - - + -
314A GLY 4.0 1.8 - - - -
315A ASN* 3.0 62.1 + - + +
317A VAL* 3.7 17.9 - - + -
324A PHE* 4.4 1.6 - + + -
325A ALA* 1.3 75.6 - - - +
327A ARG* 1.3 69.9 + - - +
334A LEU* 5.2 0.4 - - + -
335A GLN 3.3 15.0 - - - +
336A VAL* 4.2 1.8 - - + +
337A LEU* 4.4 4.0 - - - -
398A LEU* 3.8 26.5 - - + -
416A LEU* 4.0 29.2 - - + -
418A LEU* 5.2 0.9 - - + -
452A LEU* 3.7 31.6 - - + -
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Residues in contact with ARG 327 (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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33A PHE* 3.3 20.2 - - - +
35A ASP* 2.8 34.7 + - - +
73A GLU* 4.5 4.4 - - - +
74A MET* 3.2 58.4 + - - +
76A LEU* 4.6 13.0 - - - +
326A PHE* 1.3 84.0 - - - +
328A LEU* 1.3 58.3 + - - +
329A ARG* 3.9 37.4 - - - +
334A LEU* 3.7 7.4 - - - +
335A GLN* 2.9 61.2 + - + +
337A LEU* 3.8 9.8 - - + +
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Residues in contact with LEU 328 (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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35A ASP* 2.8 28.7 + - - +
326A PHE* 5.3 0.2 - - - -
327A ARG* 1.3 72.5 - - - +
329A ARG* 1.3 64.6 + - - +
330A SER* 3.3 6.4 + - - -
333A GLY* 3.8 7.0 - - - -
334A LEU* 3.8 22.9 - - + +
379A GLY* 3.8 11.7 - - - +
382A THR* 3.5 40.4 - - + +
400A THR* 4.1 8.2 + - + +
402A HIS* 4.1 13.3 - - + +
416A LEU* 4.0 33.2 - - + -
454A THR* 4.0 17.7 - - + +
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Residues in contact with ARG 329 (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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73A GLU* 3.4 22.1 + - - +
74A MET 5.2 1.6 + - - -
75A LEU* 6.3 0.8 - - - +
98A ARG* 3.8 20.8 - - - +
327A ARG* 3.8 33.7 - - - +
328A LEU* 1.3 70.8 - - - +
330A SER* 1.3 65.1 + - - +
331A SER* 3.1 13.6 + - - +
332A SER* 2.7 42.1 + - - +
333A GLY 2.9 39.0 + - - +
335A GLN* 3.8 20.1 - - - +
353A GLN* 5.7 1.8 + - - +
374A VAL* 6.2 0.2 - - - +
379A GLY* 3.3 5.8 - - - -
633A CYS* 3.9 30.2 - - - -
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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