Contacts of the helix formed by residues 33 - 43 (chain G) in PDB entry 6C3P
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 VAL 33 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C MET* 4.4 12.6 - - + -
91C TRP* 6.4 0.7 - - + -
5G PHE* 5.3 6.1 - - + -
29G ASP 3.6 7.0 - - - +
30G ALA* 2.9 16.9 + - - +
32G ASN* 1.3 76.2 - - - +
34G VAL* 1.3 69.2 + - + +
35G PRO* 3.3 2.7 - - - -
36G HIS* 3.0 7.9 + - - +
37G VAL* 3.0 37.8 + - + +
108G MET* 5.6 5.4 - - + -
109G PRO* 3.6 35.2 - - + -
112G MET* 4.0 21.1 - - + -
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Residues in contact with VAL 34 (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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88C MET* 4.0 23.6 - - + -
92C LEU* 3.7 30.5 - - + -
30G ALA 4.0 8.5 - - - +
31G LEU* 3.5 20.0 - - + +
33G VAL* 1.3 76.3 - - - +
35G PRO* 1.3 64.7 - - + +
37G VAL* 3.4 8.0 + - - +
38G PHE* 2.9 23.3 + - + +
145G LEU* 6.4 1.1 - - + -
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Residues in contact with PRO 35 (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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31G LEU 3.2 13.9 - - - +
32G ASN 3.9 7.4 - - - +
33G VAL 3.4 4.5 - - - -
34G VAL* 1.3 93.1 - - + +
36G HIS* 1.3 62.7 + - + +
38G PHE* 3.1 8.8 + - + +
39G LEU 3.0 13.2 + - - -
142G TYR* 2.8 29.4 - - + -
145G LEU* 4.0 15.7 - - + -
146G ALA* 3.9 24.2 - - + +
149G THR* 3.9 26.5 - - + +
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Residues in contact with HIS 36 (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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32G ASN 3.7 19.4 + - - -
33G VAL* 3.0 7.4 + - - +
35G PRO* 1.3 82.3 - - + +
37G VAL* 1.3 63.4 + - - +
39G LEU* 3.5 0.9 + - - +
40G LEU* 2.9 30.7 + - - +
109G PRO 3.7 7.4 + - - -
112G MET* 3.8 23.6 - - + +
113G ALA* 3.3 41.7 + - + +
116G ALA* 3.9 5.3 - - + +
142G TYR* 3.0 32.5 - + - -
146G ALA* 4.4 10.4 - - + +
150G LYS* 6.1 4.2 - - + +
179G TYR* 3.8 17.3 + - - -
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Residues in contact with VAL 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 4.9 1.3 - - + +
85C LEU* 4.6 13.9 - - + -
88C MET* 3.9 33.0 - - + -
33G VAL* 3.0 31.9 + - + +
34G VAL* 3.5 9.4 - - - +
36G HIS* 1.3 77.5 - - - +
38G PHE* 1.3 65.4 + - - +
40G LEU* 4.5 1.8 - - - -
41G PHE* 2.9 57.4 + - + +
112G MET* 5.2 9.2 - - + +
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Residues in contact with PHE 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 4.2 28.8 - - + +
34G VAL* 2.9 16.5 + - + +
35G PRO* 3.1 12.8 + - + +
37G VAL* 1.3 77.3 - - - +
39G LEU* 1.3 62.9 + - + +
41G PHE* 3.7 1.2 - - - +
42G ILE* 2.9 64.8 + - + +
138G ALA* 5.4 5.2 - - + -
141G VAL* 5.4 8.3 - - + -
142G TYR* 4.6 14.1 - + + -
145G LEU* 4.5 21.5 - - + -
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Residues in contact with LEU 39 (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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35G PRO 3.0 6.8 + - - +
36G HIS 4.1 1.6 - - - +
38G PHE* 1.3 78.6 - - + +
40G LEU* 1.3 61.2 + - - +
41G PHE 2.9 1.4 + - - -
42G ILE* 3.3 8.5 - - + +
43G THR* 2.7 59.6 + - + +
116G ALA* 3.9 21.5 - - + +
119G THR* 5.0 3.1 - - + -
120G SER* 4.3 17.0 - - - +
123G TYR* 6.0 0.7 - - + -
138G ALA* 4.9 6.3 - - + +
139G LEU* 4.5 13.7 - - + -
142G TYR* 3.4 60.6 - - + -
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Residues in contact with LEU 40 (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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36G HIS 2.9 20.5 + - - +
37G VAL* 3.8 2.9 - - - +
39G LEU* 1.3 76.9 - - - +
41G PHE* 1.3 88.0 + - + +
43G THR* 4.3 4.0 - - - -
44G PHE* 3.0 64.9 - - + +
112G MET* 4.5 21.3 - - + +
115G MET* 3.9 29.2 - - + -
116G ALA* 4.7 10.1 - - + +
119G THR* 4.9 6.3 - - - +
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Residues in contact with PHE 41 (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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77C MET* 6.0 3.4 - - + -
80C LEU* 5.4 0.7 - - + -
81C CYS* 3.4 55.8 - - + +
84C LEU* 3.5 38.1 - - + -
85C LEU* 4.9 11.0 - - + -
37G VAL* 2.9 53.8 + - + +
38G PHE 4.3 0.9 - - - +
40G LEU* 1.3 105.0 - - + +
42G ILE* 1.3 61.0 + - - +
43G THR 3.4 0.7 - - - -
44G PHE* 4.5 9.4 - + - +
45G PRO* 3.7 6.6 - - - +
112G MET* 6.4 1.6 - - - -
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Residues in contact with ILE 42 (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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85C LEU* 5.5 3.3 - - + +
38G PHE* 2.9 52.9 + - + +
39G LEU* 3.3 17.7 - - + +
41G PHE* 1.3 78.3 - - - +
43G THR* 1.3 74.4 + - + +
44G PHE 3.7 0.4 - - - -
45G PRO* 4.0 6.0 - - - +
46G ILE* 3.8 18.2 - - + +
138G ALA* 5.3 13.9 - - + -
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Residues in contact with THR 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G LEU* 2.7 36.4 + - + +
40G LEU* 4.3 0.9 - - - -
42G ILE* 1.3 95.2 - - + +
44G PHE* 1.3 67.2 + - - +
45G PRO 3.5 0.9 - - - -
46G ILE* 3.2 12.1 - - + +
47G LEU* 2.9 23.0 + - - +
119G THR* 3.5 21.1 - - - +
123G TYR* 4.0 38.0 - - + -
138G ALA* 5.5 4.7 - - + -
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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