Contacts of the strand formed by residues 333 - 341 (chain A) in PDB entry 3HIG
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 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A LEU* 4.0 6.3 - - - -
329A ARG* 2.8 45.7 + - - +
332A SER* 1.3 75.6 + - - +
334A LEU* 1.3 65.7 + - - -
335A GLN* 3.7 4.9 + - - +
352A VAL* 4.9 2.5 - - - -
378A LEU* 4.8 3.4 - - - -
379A GLY* 3.8 14.4 - - - -
454A THR* 6.0 0.7 - - - -
465A TRP* 6.5 0.9 - - - -
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Residues in contact with LEU 334 (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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326A PHE* 5.2 0.7 - - + -
327A ARG 3.7 14.8 - - - +
328A LEU* 4.0 6.7 - - + +
333A GLY* 1.3 71.5 - - - -
335A GLN* 1.3 61.8 + - - +
351A SER* 3.7 0.7 - - - -
352A VAL* 3.3 36.4 + - + +
416A LEU* 3.9 27.8 - - + -
452A LEU* 4.1 26.2 - - + +
454A THR* 3.9 26.5 - - + +
465A TRP* 3.9 27.0 - - + +
467A PHE* 3.6 32.2 - - + -
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Residues in contact with GLN 335 (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 LEU* 5.4 3.8 - - - +
326A PHE* 3.2 7.1 - - - +
327A ARG* 2.9 60.2 + - + +
329A ARG* 3.7 26.6 - - - +
332A SER* 4.3 5.7 + - - -
333A GLY 3.8 8.7 - - - +
334A LEU* 1.3 80.9 - - - +
336A VAL* 1.3 63.6 + - - +
337A LEU* 3.8 19.3 - - + +
349A GLU* 3.8 11.2 + - + +
350A VAL 3.3 11.2 - - - +
351A SER* 3.5 20.6 + - - -
353A GLN* 5.3 1.8 - - - +
467A PHE* 4.4 1.8 - - - -
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Residues in contact with VAL 336 (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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324A PHE* 4.1 16.4 - - + -
325A ALA 3.3 6.7 - - - +
335A GLN* 1.3 74.6 - - - +
337A LEU* 1.3 62.4 + - - +
339A VAL* 4.1 19.5 - - + +
349A GLU* 3.4 2.9 - - - +
350A VAL* 2.9 52.0 + - + +
452A LEU* 3.5 31.9 - - + -
467A PHE* 4.0 15.2 - - + -
469A PHE* 4.2 8.7 - - + -
475A MET* 4.4 12.8 - - + -
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Residues in contact with LEU 337 (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* 3.9 47.8 - - + -
76A LEU* 4.4 15.5 - - + -
324A PHE* 3.7 2.1 - - - +
325A ALA 2.7 33.4 + - - +
326A PHE 4.4 1.8 - - - -
327A ARG* 3.9 26.5 - - + +
335A GLN* 3.8 23.1 - - + +
336A VAL* 1.3 78.2 - - - +
338A ASN* 1.3 69.6 + - - +
339A VAL* 3.3 4.2 + - - -
348A TYR* 3.2 18.6 - - + +
349A GLU* 3.9 20.2 - - + -
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Residues in contact with ASN 338 (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* 3.7 24.0 - - + -
86A LEU* 3.7 26.4 - - - +
323A SER* 3.4 8.6 + - - +
324A PHE* 3.9 2.9 - - - -
325A ALA* 5.1 3.3 - - + +
337A LEU* 1.3 73.0 - - - +
339A VAL* 1.3 59.2 + - - +
340A HIS* 3.0 23.6 + - - -
345A ARG* 2.8 34.9 + - - +
347A ALA 3.6 5.4 + - - -
348A TYR* 2.9 20.0 + - + +
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Residues in contact with VAL 339 (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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322A TRP* 3.6 33.9 - - + -
323A SER 3.5 5.6 - - - +
324A PHE* 3.9 17.5 - - + -
336A VAL* 4.1 24.9 - - + +
337A LEU 4.0 9.4 - - - +
338A ASN* 1.3 73.3 - - - +
340A HIS* 1.3 62.6 + - - +
345A ARG* 3.5 3.3 - - - -
346A ILE* 2.8 32.0 + - + -
347A ALA* 2.8 32.8 + - + +
350A VAL* 5.1 0.4 - - + -
469A PHE* 4.4 2.5 - - + -
475A MET* 4.2 13.7 - - - -
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Residues in contact with HIS 340 (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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87A ASP* 5.4 1.0 + - - -
321A GLY 4.3 0.4 - - - +
322A TRP* 3.4 13.6 - - - -
323A SER* 2.7 46.7 + - - +
338A ASN* 3.0 50.5 + - - -
339A VAL* 1.3 74.3 - - - +
341A PHE* 1.3 59.4 + - - +
343A GLY* 3.6 21.3 + - - +
344A GLU 3.2 12.3 - - - +
345A ARG* 3.4 42.5 + - + +
346A ILE* 4.5 1.8 - - - -
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Residues in contact with PHE 341 (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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321A GLY* 3.3 28.7 - - - -
322A TRP* 3.5 40.2 - + + -
340A HIS* 1.3 73.9 - - - +
342A GLY* 1.3 68.8 + - - +
343A GLY 3.2 0.9 - - - -
344A GLU* 3.0 22.0 + - - +
346A ILE* 4.0 12.2 - - + +
471A PRO 3.3 27.4 - - - -
473A GLY* 3.5 18.8 - - - -
593A TYR* 4.5 3.1 - - - +
701A PHE* 4.7 1.0 - - - -
702A PHE* 3.3 34.9 - + + -
706A PRO* 3.5 24.9 - - + -
291B PHE* 3.9 11.9 - + - -
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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