Contacts of the strand formed by residues 439 - 447 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G VAL* 3.2 18.9 - - - +
117G ILE 4.2 1.6 - - - +
118G ARG* 4.1 29.5 - - + +
136G GLN* 5.3 0.5 - - - +
148G THR* 3.3 17.7 + - - +
149G VAL* 2.9 34.1 - - + +
427G ILE* 4.2 8.1 - - + -
428G ARG 3.5 9.4 - - - +
430G ARG 2.8 31.7 + - - +
438G TRP* 1.3 72.2 - - - +
440G SER* 1.3 65.2 + - - +
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Residues in contact with SER 440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G ILE* 4.1 7.1 - - - +
115G PHE 4.2 1.7 + - - -
116G VAL* 3.4 15.1 - - - -
117G ILE* 2.9 32.8 + - - +
118G ARG* 4.4 4.7 - - - -
140G LEU* 3.9 20.0 - - - +
427G ILE* 3.5 6.6 - - - +
428G ARG 3.0 30.5 + - - +
438G TRP* 3.8 7.4 - - - -
439G THR* 1.3 78.6 - - - +
441G GLY* 1.3 66.1 + - - +
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Residues in contact with GLY 441 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G SER* 3.3 14.0 + - - -
106G ILE* 3.8 7.4 - - - +
117G ILE* 3.1 30.8 + - - +
120G PRO* 5.8 0.2 - - - -
425G GLU* 4.6 11.7 - - - -
426G LEU 3.1 11.9 - - - -
427G ILE* 4.4 1.6 - - - -
440G SER* 1.3 83.8 + - - +
442G SER* 1.3 61.9 + - - -
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Residues in contact with SER 442 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G LYS* 5.9 1.3 - - - -
103G ASP* 3.4 12.1 + - - -
104G ASN* 3.9 5.2 - - - -
105G SER* 3.4 15.9 + - - -
106G ILE 3.5 9.4 + - - -
117G ILE* 6.0 0.4 - - - -
120G PRO* 4.8 1.8 - - - +
425G GLU* 3.4 6.6 - - - +
426G LEU* 2.7 45.1 + - - -
441G GLY* 1.3 75.3 - - - -
443G SER* 1.3 60.6 + - - +
460G ASP* 3.2 29.8 + - - -
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Residues in contact with SER 443 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G SER* 5.2 1.9 + - - -
102G LYS* 3.3 5.5 - - - +
103G ASP* 2.5 51.4 + - - +
120G PRO* 4.7 17.9 - - - -
122G ILE* 6.1 3.8 - - - +
131G THR* 4.8 10.8 - - - +
164G GLY 5.9 0.3 + - - -
423G TRP* 5.6 4.3 - - - -
424G VAL 3.3 10.1 - - - -
426G LEU* 4.7 1.8 - - - -
442G SER* 1.3 80.5 - - - +
444G ILE* 1.3 70.0 + - - +
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Residues in contact with ILE 444 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G VAL* 6.3 0.7 - - + -
101G SER* 3.2 12.3 - - - +
102G LYS* 3.7 21.1 - - + -
122G ILE* 5.6 0.4 - - - -
397G ILE* 3.9 12.3 - - + -
398G VAL* 3.9 19.3 - - + -
423G TRP* 3.1 5.7 - - - +
424G VAL* 2.8 52.0 + - + +
426G LEU* 4.1 13.9 - - + -
443G SER* 1.3 80.5 - - - +
445G SER* 1.3 62.7 + - - +
446G PHE* 4.0 14.8 - - + -
458G TRP* 3.8 33.0 - - + +
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Residues in contact with SER 445 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G VAL* 4.0 0.7 - - - +
100G TYR* 2.9 38.1 + - - +
101G SER* 2.6 29.3 + - - +
122G ILE* 3.5 25.0 - - - +
410G PHE* 4.0 7.2 - - - -
422G PHE 3.1 11.4 - - - -
423G TRP* 4.1 0.9 - - - -
444G ILE* 1.3 76.7 - - - +
446G PHE* 1.3 74.4 + - - +
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Residues in contact with PHE 446 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G TRP* 4.1 14.8 - - + -
98G ALA* 3.3 11.2 - - - +
99G VAL* 3.4 39.3 - - + -
100G TYR* 4.0 2.7 - - - -
395G GLN* 5.8 0.9 - - - -
397G ILE* 3.9 30.5 - - + -
410G PHE* 4.1 0.2 - - - -
421G CYS* 3.0 6.1 - - - +
422G PHE* 2.8 66.7 + + + -
444G ILE* 4.0 21.3 - - + -
445G SER* 1.3 90.8 - - - +
447G CYS* 1.3 64.9 + - - +
458G TRP* 3.6 41.3 - + - -
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Residues in contact with CYS 447 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F ILE* 4.2 15.5 - - + -
97G TRP* 3.6 7.3 - - - -
98G ALA 3.1 22.3 + - - +
100G TYR* 4.2 14.3 - - - +
410G PHE* 4.2 4.7 - - - -
412G GLN* 3.1 19.7 - - - -
419G ARG* 4.0 12.1 - - - +
420G PRO 3.6 1.3 - - - -
421G CYS* 2.1 46.2 - - - +
446G PHE* 1.3 76.3 - - - +
448G GLY* 1.3 72.0 + - - +
449G VAL* 4.0 3.7 - - + +
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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