Contacts of the strand formed by residues 407 - 411 (chain D) 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 SER 407 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350D LYS* 3.2 16.4 + - - +
351D GLY* 3.2 24.9 + - - +
352D PHE* 3.6 13.4 - - - -
363D GLY 5.2 1.0 - - - -
374D PHE* 3.5 37.7 - - - -
405D GLY 4.6 0.5 + - - -
406D TYR* 1.3 78.4 - - - +
408D GLY* 1.3 57.5 + - - +
423D TRP* 3.1 23.6 - - - -
424D VAL* 4.2 2.5 - - - -
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Residues in contact with GLY 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D SER* 4.8 1.1 - - - -
279D SER* 3.7 11.4 - - - -
350D LYS* 4.5 1.1 - - - -
352D PHE* 4.0 8.7 - - - -
407D SER* 1.3 75.4 - - - +
409D SER* 1.3 61.3 + - - -
422D PHE* 3.2 4.7 - - - +
423D TRP* 3.0 56.9 + - - -
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Residues in contact with SER 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ILE 4.6 0.3 - - - +
228D SER* 4.7 6.5 + - - -
229D GLU* 3.9 14.2 + - - +
279D SER* 3.5 26.7 + - - -
280D CYS 4.1 7.4 + - - +
281D TYR* 4.3 10.5 - - - +
352D PHE* 3.8 15.5 - - - +
353D SER 5.7 0.4 - - - -
354D PHE* 3.5 28.7 - - - -
408D GLY* 1.3 75.5 - - - -
410D PHE* 1.3 65.1 + - - +
421D CYS 3.6 4.5 - - - -
422D PHE* 4.3 1.3 - - - +
423D TRP* 4.1 4.9 + - - -
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Residues in contact with PHE 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D TYR* 4.4 10.5 - + - -
122D ILE* 3.2 58.1 - - + +
124D CYS* 4.1 18.6 - - - -
129D CYS* 5.0 0.4 - - - -
229D GLU* 3.0 12.6 - - - +
354D PHE* 4.7 0.5 - - - -
409D SER* 1.3 74.6 - - - +
411D VAL* 1.2 69.6 + - - +
412D GLN* 5.0 1.1 - - + -
420D PRO* 4.2 0.2 - - - +
421D CYS* 2.9 72.3 + - + +
422D PHE* 3.4 25.6 - - - -
423D TRP* 3.8 11.7 - + + -
445D SER* 4.0 13.2 - - - -
446D PHE 4.2 0.2 - - - -
447D CYS* 4.2 6.1 - - - -
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Residues in contact with VAL 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D LEU* 5.5 0.4 - - + -
124D CYS* 3.9 27.2 + - - +
229D GLU* 3.1 14.4 + - - +
281D TYR* 3.7 30.1 - - + -
282D PRO* 3.8 12.3 - - + -
354D PHE* 5.2 3.4 - - + -
410D PHE* 1.2 80.4 - - - +
412D GLN* 1.3 110.7 - - - +
418D ILE* 3.0 28.5 - - + -
419D ARG 3.5 7.2 - - - +
420D PRO* 5.2 3.6 - - + -
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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