Contacts of the strand formed by residues 439 - 447 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B VAL* 3.2 18.9 - - - +
117B ILE 4.2 1.1 - - - +
118B ARG* 4.3 22.0 - - + +
148B THR* 3.2 23.7 + - - +
149B VAL* 3.0 24.8 - - + +
427B ILE* 4.0 14.8 - - + -
428B ARG 3.3 10.8 - - - +
430B ARG 2.8 30.6 + - - +
438B TRP* 1.3 71.5 - - - +
440B SER* 1.3 70.5 + - - +
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Residues in contact with SER 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 3.8 6.7 - - - +
115B PHE 4.1 1.9 + - - -
116B VAL* 3.3 9.2 - - - -
117B ILE* 2.9 36.4 + - - +
118B ARG* 4.6 4.0 - - - -
140B LEU* 3.8 27.5 - - - +
427B ILE* 3.6 3.3 - - - +
428B ARG* 2.7 31.1 + - - -
438B TRP* 3.7 6.8 - - - -
439B THR* 1.3 78.8 - - - +
441B GLY* 1.3 63.4 + - - +
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Residues in contact with GLY 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASP* 5.4 0.2 - - - +
105B SER* 3.3 11.4 + - - -
106B ILE* 3.6 9.8 - - - +
117B ILE* 3.3 32.5 + - - +
118B ARG* 4.7 0.4 - - - +
120B PRO* 5.8 0.2 - - - -
425B GLU* 4.7 10.5 - - - -
426B LEU 3.2 13.0 - - - -
427B ILE* 4.3 1.8 - - - -
440B SER* 1.3 82.9 + - - +
442B SER* 1.3 60.8 + - - -
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Residues in contact with SER 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LYS* 5.7 1.3 - - - -
103B ASP* 3.6 3.9 + - - -
104B ASN* 3.9 5.7 - - - -
105B SER* 3.3 29.7 + - - -
106B ILE* 3.5 4.9 + - - +
117B ILE* 5.8 0.4 - - - -
120B PRO* 4.7 1.8 - - - +
425B GLU* 3.4 6.8 - - - +
426B LEU* 2.8 45.6 + - - -
441B GLY* 1.3 73.5 - - - -
443B SER* 1.3 64.0 + - - +
460B ASP* 2.8 26.8 + - - -
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Residues in contact with SER 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B SER* 5.2 3.6 + - - -
102B LYS* 3.4 1.6 - - - +
103B ASP* 2.5 55.1 + - - +
120B PRO* 4.7 17.9 - - - -
122B ILE* 6.2 2.9 - - - -
131B THR* 4.9 10.1 + - - +
164B GLY 5.8 0.9 + - - -
423B TRP* 5.6 5.8 - - - -
424B VAL 3.3 10.3 - - - -
426B LEU* 4.7 1.1 - - - +
442B SER* 1.3 77.6 - - - +
444B ILE* 1.3 69.3 + - - +
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Residues in contact with ILE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 5.8 1.6 - - + -
101B SER* 3.1 9.4 - - - +
102B LYS* 3.5 28.0 - - + -
397B ILE* 3.7 30.1 - - + -
398B VAL* 3.8 9.4 - - + -
423B TRP* 3.3 4.0 - - - +
424B VAL* 2.9 46.5 + - + +
426B LEU* 4.1 11.4 - - + -
443B SER* 1.3 80.9 - - - +
445B SER* 1.3 61.5 + - - +
446B PHE* 3.9 13.9 - - + -
458B TRP* 3.7 31.4 - - + +
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Residues in contact with SER 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 3.8 1.6 - - - +
100B TYR* 2.6 41.7 + - - -
101B SER* 2.5 39.3 + - - +
122B ILE* 3.5 23.9 - - - +
410B PHE* 4.1 5.6 - - - -
422B PHE 3.3 13.2 - - - -
423B TRP* 4.1 1.3 - - - -
444B ILE* 1.3 77.4 - - - +
446B PHE* 1.3 65.3 + - - +
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Residues in contact with PHE 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B TRP* 3.9 22.0 - - + -
98B ALA* 3.0 11.7 - - - +
99B VAL* 3.3 42.6 - - + -
100B TYR* 3.9 2.2 - - - -
395B GLN* 5.5 1.3 - - - -
397B ILE* 3.9 23.6 - - + -
410B PHE* 4.4 0.7 - - - -
421B CYS* 2.9 22.6 - - - +
422B PHE* 3.0 39.3 + + + -
444B ILE* 3.9 27.4 - - + -
445B SER* 1.3 81.4 - - - +
447B CYS* 1.3 65.3 + - - +
458B TRP* 3.6 36.1 - + - -
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Residues in contact with CYS 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B TRP* 3.4 8.7 - - - -
98B ALA* 3.0 24.6 + - - -
100B TYR* 4.2 18.8 - - - +
410B PHE* 4.3 1.1 - - - -
412B GLN* 3.1 18.6 - - - -
419B ARG* 4.3 11.4 - - - +
420B PRO 3.6 2.0 - - - -
421B CYS* 2.1 43.5 - - - +
446B PHE* 1.3 74.8 - - - +
448B GLY* 1.3 72.5 + - - +
449B VAL* 4.1 2.6 - - + +
211D ILE* 4.0 17.0 - - + -
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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