Contacts of the strand formed by residues 43 - 48 (chain G) in PDB entry 3HOU
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 43 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38G CYS* 3.6 6.0 - - - -
39G THR* 2.8 36.7 + - - -
40G GLY 4.0 2.0 + - - -
41G LYS 3.5 1.2 - - - -
42G PHE* 1.3 82.5 - - - +
44G TYR* 1.3 62.9 + - - -
45G ILE* 3.5 4.5 + - - +
79G PHE 3.9 7.4 - - - -
80G LYS* 3.9 10.7 - - - +
157G ILE* 4.0 10.1 - - - -
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Residues in contact with TYR 44 (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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140D ASP* 3.6 31.6 - - + -
37G SER 3.8 5.4 - - - +
38G CYS* 3.4 16.6 - - + -
43G GLY* 1.3 69.9 - - - -
45G ILE* 1.3 60.5 + - - +
46G LEU* 3.6 13.4 + - + +
78G VAL* 3.0 7.8 - - - +
79G PHE* 2.7 56.6 + + + +
81G PRO* 5.3 0.2 - - + -
105G PRO* 3.7 34.2 + - + -
106G MET* 3.8 14.6 - - + -
155G SER 4.8 3.4 - - - -
156G SER* 3.1 27.3 - - - -
157G ILE* 3.2 39.6 + - + -
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Residues in contact with ILE 45 (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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5D THR* 4.7 8.3 - - + +
140D ASP* 5.8 0.2 - - - +
7G LEU* 3.2 33.2 - - + -
34G VAL* 3.1 31.9 - - + +
35G GLU* 4.1 4.7 - - + -
36G GLY* 2.9 28.1 + - - -
37G SER* 3.1 23.4 + - - +
38G CYS* 6.1 0.2 - - - -
39G THR* 5.9 0.7 - - - +
42G PHE* 5.0 7.2 - - + -
43G GLY 3.5 5.5 + - - +
44G TYR* 1.3 69.9 - - - +
46G LEU* 1.3 64.2 + - - +
47G CYS 4.7 0.2 - - - +
48G VAL* 5.2 0.2 - - + -
74G TYR* 3.4 14.6 - - + +
76G ALA* 4.7 10.8 - - + -
78G VAL* 3.6 16.8 - - + -
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Residues in contact with LEU 46 (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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138D ASN* 4.0 2.7 - - - +
140D ASP* 3.8 26.9 - - + -
141D LEU* 3.3 33.5 - - + +
144D THR* 3.4 41.1 - - + +
2G PHE* 3.7 20.4 - - + -
35G GLU* 3.8 14.0 - - - +
36G GLY 4.8 0.4 - - - +
44G TYR* 4.1 14.1 - - + +
45G ILE* 1.3 75.6 - - - +
47G CYS* 1.3 61.7 + - - +
77G VAL* 3.0 22.1 + - + +
79G PHE* 3.8 13.9 - - + +
105G PRO* 3.9 10.5 - - + -
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Residues in contact with CYS 47 (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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59D ILE* 4.3 20.4 - - + -
62D ALA* 4.3 6.1 - - - -
63D LEU* 3.6 26.7 - - - -
66D ARG* 4.2 0.4 - - - -
141D LEU* 3.9 18.6 - - + -
35G GLU* 3.5 3.6 - - - -
45G ILE* 4.7 0.8 - - - +
46G LEU* 1.3 82.6 - - - +
48G VAL* 1.3 74.9 + - - +
49G LEU* 3.4 16.3 + - - +
76G ALA* 3.3 3.7 - - - +
77G VAL* 2.9 31.6 + - + -
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Residues in contact with VAL 48 (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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62D ALA* 4.5 2.4 - - - +
66D ARG* 2.9 20.4 + - - -
30G LEU* 4.4 4.9 - - + -
31G LEU* 3.2 35.4 - - + -
34G VAL* 4.3 9.6 - - + -
35G GLU* 2.8 24.2 + - + +
45G ILE* 5.2 0.2 - - + -
47G CYS* 1.3 75.7 - - - +
49G LEU* 1.3 70.2 + - - +
51G TYR* 4.9 2.8 + - - -
54G ILE* 4.5 6.1 - - + -
74G TYR* 3.5 42.6 - - + -
75G ARG 3.7 4.5 - - - +
76G ALA* 3.8 6.7 - - + -
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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