Contacts of the helix formed by residues 42 - 50 (chain G) in PDB entry 2H4C
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 ASP 42 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25G TYR* 3.4 12.6 - - + +
26G GLY* 3.3 11.9 - - - -
27G CYS 2.6 27.3 + - - -
28G TYR* 3.3 20.0 + - - +
29G CYS* 3.4 12.0 + - - -
37G PRO* 3.2 25.9 - - + +
38G GLN* 3.6 6.5 + - + +
39G ASP* 3.2 19.2 + - - +
41G THR* 1.3 77.3 - - - +
43G ARG* 1.3 59.4 + - - +
44G CYS 3.4 0.4 - - - -
45G CYS* 3.5 4.4 - - - +
46G PHE* 3.4 17.7 + - - +
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Residues in contact with ARG 43 (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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37G PRO* 4.0 21.7 + - + +
38G GLN 5.5 0.4 + - - -
39G ASP* 3.5 12.4 + - - +
40G ALA* 3.0 53.2 + - - +
41G THR 3.1 0.6 - - - -
42G ASP* 1.3 77.5 - - - +
44G CYS* 1.3 60.0 + - - +
45G CYS 2.9 5.4 - - - -
46G PHE* 4.1 9.9 - - + +
47G VAL* 2.9 39.4 + - + +
105G CYS* 4.9 1.6 - - - -
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Residues in contact with CYS 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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40G ALA 3.7 5.6 - - - -
41G THR* 3.6 3.1 + - - -
42G ASP 3.4 0.4 - - - -
43G ARG* 1.3 78.2 - - - +
45G CYS* 1.3 57.7 + - - +
47G VAL* 4.5 4.2 - - - +
48G HIS* 3.1 24.9 + - - +
102G ALA* 3.9 11.4 - - - +
105G CYS* 2.0 50.3 - - + -
106G LEU* 2.9 51.6 - - + +
109G ASN* 3.6 8.5 - - - -
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Residues in contact with CYS 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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5G PHE* 6.2 4.5 - - - -
22G TYR* 5.2 3.8 - - - -
28G TYR* 4.2 1.8 - - - -
29G CYS* 2.0 63.7 - - - +
41G THR 4.2 0.4 - - - -
42G ASP 3.5 6.5 + - - +
43G ARG 2.9 0.4 - - - -
44G CYS* 1.3 81.9 - - - +
46G PHE* 1.3 54.0 + - - +
48G HIS* 3.6 6.6 + - - +
49G ASP* 2.6 40.4 + - - +
106G LEU* 4.0 21.5 - - - -
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Residues in contact with PHE 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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28G TYR* 3.8 45.1 - + + +
37G PRO* 4.7 10.1 - - + -
42G ASP 3.4 6.0 + - - +
43G ARG* 3.1 14.2 + - + +
45G CYS* 1.3 76.3 - - - +
47G VAL* 1.3 68.2 + - + +
48G HIS 3.0 2.1 + - - -
49G ASP* 3.8 3.1 - - - -
50G CYS* 3.2 46.7 + - - -
131G GLU* 3.5 34.1 - - + -
132G GLN 3.9 19.5 - - - -
133G CYS* 4.1 1.6 - - - -
70H LEU* 4.0 16.6 - - + -
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Residues in contact with VAL 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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43G ARG* 2.9 31.6 + - + +
44G CYS* 4.6 4.7 - - - +
46G PHE* 1.3 81.4 - - + +
48G HIS* 1.3 58.2 + - - +
50G CYS* 4.4 4.0 - - - +
51G CYS* 3.4 18.9 + - - +
101G ALA* 6.6 0.4 - - + -
105G CYS* 6.2 1.3 - - - -
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Residues in contact with HIS 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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2G PHE* 4.6 4.0 - + - -
5G PHE* 3.5 24.7 - + + -
44G CYS 3.1 21.0 + - - +
45G CYS* 3.7 5.9 + - - +
46G PHE 3.0 0.4 - - - -
47G VAL* 1.3 79.5 - - - +
49G ASP* 1.3 75.3 + - - +
51G CYS* 3.1 18.0 - - - +
52G TYR* 3.1 51.0 + + - -
98G CYS* 3.5 22.0 - - + +
99G ASP* 3.3 10.3 + - - -
102G ALA* 3.4 26.7 - - + -
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Residues in contact with ASP 49 (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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28G TYR* 3.6 27.0 - - - +
45G CYS* 2.6 31.9 + - - +
46G PHE* 3.3 5.4 + - - +
48G HIS* 1.3 82.5 + - - +
50G CYS* 1.3 65.7 + - - +
52G TYR* 2.9 22.1 + - - +
53G GLY* 3.3 6.6 + - - -
69H LYS* 3.5 33.6 + - + +
70H LEU* 4.1 24.4 - - + +
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Residues in contact with CYS 50 (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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46G PHE* 3.2 30.4 + - - +
47G VAL* 4.4 4.7 - - - +
49G ASP* 1.3 79.8 - - - +
51G CYS* 1.3 57.4 + - - +
53G GLY* 2.8 20.9 + - - +
54G THR* 3.3 12.4 + - - +
133G CYS* 2.0 61.0 - - + -
70H LEU* 3.7 9.8 - - - +
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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