Contacts of the strand formed by residues 439 - 447 (chain F) 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 THR 439 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116F VAL* 3.2 20.4 - - - +
117F ILE 4.0 3.3 - - - +
118F ARG* 4.3 21.7 - - + +
136F GLN* 5.2 0.3 - - - +
148F THR* 3.0 26.2 + - - +
149F VAL* 3.0 26.8 - - + +
427F ILE* 4.2 16.6 - - + -
428F ARG 3.6 5.2 - - - +
430F ARG 2.9 27.6 + - - +
438F TRP* 1.3 75.5 + - - +
440F SER* 1.3 63.2 + - - +
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Residues in contact with SER 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F SER* 5.7 0.2 + - - -
106F ILE* 4.0 7.8 - - - +
115F PHE 4.1 2.6 + - - -
116F VAL* 3.6 8.0 - - - -
117F ILE* 3.0 29.9 + - - +
118F ARG* 4.5 4.7 - - - -
140F LEU* 3.8 15.5 - - - +
427F ILE* 3.4 5.0 - - - +
428F ARG* 2.7 39.5 + - - +
438F TRP* 3.7 18.1 - - - -
439F THR* 1.3 78.2 - - - +
441F GLY* 1.3 64.4 + - - +
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Residues in contact with GLY 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F SER* 3.2 15.9 + - - -
106F ILE* 3.7 6.5 - - - +
117F ILE* 3.4 27.2 + - - +
118F ARG* 5.1 0.4 - - - -
120F PRO* 5.8 1.8 - - - -
425F GLU* 4.7 11.0 - - - -
426F LEU 3.2 11.9 - - - -
427F ILE* 4.3 1.6 - - - -
440F SER* 1.3 83.8 + - - +
442F SER* 1.3 62.6 + - - -
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Residues in contact with SER 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LYS* 5.7 1.8 - - - -
103F ASP* 3.9 10.5 - - - -
104F ASN* 4.4 4.7 - - - -
105F SER* 3.7 5.8 + - - -
106F ILE* 3.3 20.8 + - - +
117F ILE* 6.2 0.4 - - - -
120F PRO* 4.6 2.3 - - - +
425F GLU* 3.2 8.3 - - - +
426F LEU* 2.7 44.2 + - - -
441F GLY* 1.3 72.3 - - - -
443F SER* 1.3 62.5 + - - +
460F ASP* 2.6 30.6 + - - -
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Residues in contact with SER 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F SER* 5.3 1.8 + - - -
102F LYS* 3.5 1.7 - - - +
103F ASP* 2.7 48.7 + - - +
120F PRO* 4.7 16.3 - - - +
122F ILE* 5.7 6.1 - - - +
131F THR* 4.7 12.8 + - - +
164F GLY 6.0 0.2 + - - -
423F TRP* 5.4 5.8 - - - -
424F VAL 3.1 12.3 - - - -
426F LEU* 4.9 0.4 - - - -
442F SER* 1.3 79.6 - - - +
444F ILE* 1.3 73.4 + - - +
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Residues in contact with ILE 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F VAL* 6.0 0.4 - - + -
101F SER* 3.1 11.9 - - - +
102F LYS* 3.5 24.2 - - + -
122F ILE* 5.5 0.4 - - - -
397F ILE* 3.9 16.8 - - + +
398F VAL* 3.8 20.9 - - + -
423F TRP* 3.3 2.7 - - - +
424F VAL* 2.8 47.9 + - + +
426F LEU* 4.2 13.9 - - + -
443F SER* 1.3 82.1 - - - +
445F SER* 1.3 60.2 + - - +
446F PHE* 4.0 13.2 - - + -
458F TRP* 3.7 30.7 - - + +
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Residues in contact with SER 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F VAL* 3.8 1.2 - - - +
100F TYR* 2.8 36.8 + - - -
101F SER* 2.6 36.7 + - - +
122F ILE* 3.4 27.6 - - - +
410F PHE* 3.8 7.6 - - - -
422F PHE 3.1 13.2 - - - -
423F TRP* 4.0 0.9 - - - -
444F ILE* 1.3 75.0 - - - +
446F PHE* 1.3 66.6 + - - +
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Residues in contact with PHE 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F TRP* 4.0 17.7 - - + -
98F ALA 3.0 12.3 - - - +
99F VAL* 3.4 34.8 - - + -
100F TYR* 3.9 2.0 - - - -
395F GLN* 5.4 1.1 - - - -
397F ILE* 3.9 29.8 - - + -
410F PHE* 4.2 0.3 - - - -
421F CYS* 3.0 6.6 - - - +
422F PHE* 2.9 63.8 + + + +
444F ILE* 4.0 21.1 - - + -
445F SER* 1.3 81.3 - - - +
447F CYS* 1.3 62.9 + - - +
458F TRP* 3.4 43.3 - + - -
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Residues in contact with CYS 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F TRP* 4.0 4.9 - - - -
98F ALA* 2.9 22.2 + - - +
100F TYR* 4.2 18.3 - - - +
410F PHE* 4.2 2.7 - - - -
412F GLN* 2.6 19.7 - - - +
419F ARG* 4.0 10.3 - - - +
420F PRO 3.8 0.9 - - - -
421F CYS* 2.1 46.9 - - - +
446F PHE* 1.3 75.8 - - - +
448F GLY* 1.3 70.6 + - - +
449F VAL* 3.8 5.4 - - + +
211H ILE* 4.1 15.7 - - + -
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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