Contacts of the strand formed by residues 359 - 364 (chain E) in PDB entry 2HU4
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 359 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355E LYS* 3.6 1.0 - - - +
356E TYR 2.9 31.1 + - - -
357E GLY 4.1 1.2 - - - +
358E ASN* 1.3 81.4 - - - +
360E VAL* 1.3 67.5 + - - +
378E TRP* 3.8 10.1 - - - -
379E ASP 3.3 3.8 - - - -
380E PRO* 3.6 6.3 - - - -
381E ASN* 3.1 18.6 + - - +
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Residues in contact with VAL 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E ILE* 4.8 3.1 - - + -
353E SER* 5.1 4.3 - - - -
354E PHE 3.2 11.2 - - - +
355E LYS* 4.1 0.9 - - - -
359E GLY* 1.3 79.3 - - - +
361E TRP* 1.3 60.1 + - - +
362E ILE* 3.8 26.7 + - + +
377E ILE 3.5 1.7 - - - +
378E TRP* 3.2 10.7 - - - -
379E ASP* 3.0 34.6 + - + +
382E GLY* 3.7 25.8 - - - +
383E TRP* 3.0 44.4 - - + -
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Residues in contact with TRP 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ILE* 3.3 34.9 + - + +
95E ASN* 3.8 28.5 - - - -
96E GLY* 4.4 2.0 - - - -
97E TRP* 3.4 44.2 - + + -
352E PHE* 5.2 0.3 - - - -
353E SER* 3.2 9.7 + - - -
354E PHE* 2.7 40.2 + - + +
356E TYR* 4.1 11.4 - + - -
360E VAL* 1.3 71.7 - - - +
362E ILE* 1.3 59.4 + - - +
363E GLY 4.2 0.2 + - - -
376E MET* 3.8 24.5 - - + +
377E ILE 3.2 38.8 - - - -
378E TRP* 3.7 40.1 - + + -
392E VAL* 4.3 14.6 - - + -
395E GLN* 4.9 2.9 - - + -
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Residues in contact with ILE 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E ARG* 6.3 0.9 - - - -
317E ILE* 4.6 9.9 - - + -
319E SER* 4.4 13.9 - - - +
321E VAL* 3.8 27.4 - - + +
323E GLY* 4.3 20.4 - - - +
352E PHE 4.9 0.2 - - - +
353E SER* 3.7 16.8 - - - +
360E VAL* 3.9 27.4 - - + +
361E TRP* 1.3 77.0 - - - +
363E GLY* 1.3 72.7 + - - +
364E ARG* 4.0 9.0 + - + +
375E GLU 3.4 2.1 - - - +
376E MET* 3.3 7.8 - - - -
377E ILE* 2.8 47.7 + - + +
379E ASP* 4.9 5.4 - - + -
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Residues in contact with GLY 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300E ARG* 4.9 5.4 + - - -
323E GLY 4.1 6.1 - - - +
351E GLY* 5.4 0.5 - - - -
352E PHE* 3.9 24.7 + - - +
361E TRP 4.2 0.8 + - - -
362E ILE* 1.3 77.0 - - - +
364E ARG* 1.3 63.3 + - - +
374E PHE* 3.6 16.1 - - - -
375E GLU 3.4 7.6 - - - -
376E MET* 3.5 17.0 - - - +
407E SER* 4.9 3.1 + - - -
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Residues in contact with ARG 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321E VAL* 3.5 16.9 - - - +
322E PHE 2.8 27.4 + - - -
323E GLY* 3.7 20.9 - - - +
327E ARG* 3.5 24.3 - - - +
330E ASP* 3.0 38.8 + - - -
362E ILE* 4.5 5.6 - - + +
363E GLY* 1.3 75.3 - - - +
365E THR* 1.3 66.5 + - - +
374E PHE* 3.3 12.9 - - - -
375E GLU* 2.9 60.8 + - + +
377E ILE* 3.4 16.1 - - + +
390E PHE* 5.4 1.6 - - - -
394E LYS* 4.8 4.4 - - - +
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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