Contacts of the helix formed by residues 33 - 43 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A MET* 4.3 13.7 - - + -
91A TRP* 6.2 0.9 - - + -
5E PHE* 5.3 5.6 - - + -
29E ASP 3.6 7.4 - - - +
30E ALA* 2.9 17.1 + - - +
32E ASN* 1.3 75.9 - - - +
34E VAL* 1.3 67.3 - - - +
35E PRO* 3.3 2.5 - - - -
36E HIS* 3.0 8.4 + - - +
37E VAL* 3.0 38.2 + - + +
108E MET* 5.1 5.6 - - + -
109E PRO* 3.6 34.8 - - + -
112E MET* 4.0 21.8 - - + -
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Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A MET* 4.0 23.6 - - + -
92A LEU* 3.6 32.1 - - + -
30E ALA 4.0 8.3 - - - +
31E LEU* 3.5 19.5 - - + +
33E VAL* 1.3 77.9 - - - +
35E PRO* 1.3 66.0 - - + +
37E VAL* 3.4 8.7 + - - +
38E PHE* 2.9 22.9 + - + +
145E LEU* 6.4 1.3 - - + -
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Residues in contact with PRO 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU 3.2 13.9 - - - +
32E ASN 3.9 6.7 - - - +
33E VAL 3.4 4.3 - - - -
34E VAL* 1.3 93.8 - - + +
36E HIS* 1.3 64.2 + - + +
38E PHE* 3.1 9.1 + - + +
39E LEU 3.0 13.5 + - - -
142E TYR* 2.8 30.0 - - + -
145E LEU* 4.0 15.0 - - + -
146E ALA* 3.9 24.5 - - + +
149E THR* 4.0 27.6 - - + +
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Residues in contact with HIS 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ASN 3.7 19.5 + - - -
33E VAL* 3.0 7.0 + - - +
35E PRO* 1.3 83.7 - - + +
37E VAL* 1.3 62.9 - - - +
39E LEU* 4.0 1.2 - - - +
40E LEU* 2.9 29.7 + - - +
109E PRO* 3.7 7.7 + - + -
112E MET* 3.7 24.3 - - + +
113E ALA* 3.3 41.3 + - + +
116E ALA* 3.9 5.1 - - + +
142E TYR* 3.0 32.1 - + - -
146E ALA* 4.4 9.0 - - + +
150E LYS* 6.1 3.8 - - + +
179E TYR* 3.8 18.8 + + - -
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Residues in contact with VAL 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU 4.9 1.3 - - - +
85A LEU* 4.7 13.7 - - + -
88A MET* 3.8 33.9 - - + -
33E VAL* 3.0 31.4 + - + +
34E VAL* 3.5 9.4 - - - +
36E HIS* 1.3 76.7 - - - +
38E PHE* 1.3 64.4 + - - +
40E LEU* 4.5 2.2 - - - -
41E PHE* 2.9 58.1 + - + +
112E MET* 5.2 9.4 - - + +
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Residues in contact with PHE 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 4.2 29.3 - - + +
34E VAL* 2.9 16.9 + - + +
35E PRO* 3.1 13.7 + - + +
37E VAL* 1.3 77.8 - - - +
39E LEU* 1.3 63.6 + - + +
41E PHE* 3.7 0.7 - - - +
42E ILE* 2.9 65.0 + - + +
138E ALA* 5.4 6.5 - - + -
141E VAL* 5.4 8.5 - - + -
142E TYR* 4.6 13.9 - + + -
145E LEU* 4.5 22.4 - - + -
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Residues in contact with LEU 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E PRO 3.0 6.6 + - - +
36E HIS 4.1 1.3 - - - +
38E PHE* 1.3 78.2 - - + +
40E LEU* 1.3 59.7 + - - +
41E PHE 2.9 1.4 + - - -
42E ILE* 3.0 9.1 + - + +
43E THR* 2.7 60.5 + - + +
116E ALA* 3.9 21.5 - - + +
119E THR* 5.0 2.7 - - + -
120E SER* 4.3 17.5 - - - +
123E TYR* 6.0 0.2 - - + -
138E ALA* 4.9 6.1 - - + +
139E LEU* 4.5 13.2 - - + -
142E TYR* 3.4 60.8 - - + +
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Residues in contact with LEU 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E HIS 2.9 20.1 + - - +
37E VAL* 3.8 2.9 - - - +
39E LEU* 1.3 77.3 - - - +
41E PHE* 1.3 88.0 + - + +
43E THR* 4.3 4.5 - - - -
44E PHE* 3.0 64.3 - - + +
112E MET* 4.5 20.4 - - - +
115E MET* 3.9 29.8 - - + -
116E ALA* 4.7 9.8 - - + +
119E THR* 4.9 5.8 - - - +
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Residues in contact with PHE 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A MET* 6.1 2.9 - - + -
80A LEU* 6.1 0.7 - - + -
81A CYS* 3.4 55.9 - - + +
84A LEU* 3.4 39.3 - - + -
85A LEU* 4.9 10.3 - - + -
37E VAL* 2.9 52.8 + - + +
38E PHE 4.3 1.1 - - - +
40E LEU* 1.3 105.2 - - + +
42E ILE* 1.3 61.3 + - - +
43E THR 3.4 1.1 - - - -
44E PHE* 4.5 8.7 - + - +
45E PRO* 3.7 6.2 - - - +
112E MET* 6.4 2.0 - - - -
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Residues in contact with ILE 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 5.4 4.0 - - + +
38E PHE* 2.9 52.7 + - + +
39E LEU* 3.3 17.7 - - + +
41E PHE* 1.3 78.7 - - - +
43E THR* 1.3 73.5 + - + +
45E PRO* 4.0 6.0 - - - +
46E ILE* 3.8 17.8 - - + +
138E ALA* 5.3 13.0 - - + -
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Residues in contact with THR 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU* 2.7 35.3 + - + +
40E LEU* 4.3 0.7 - - - -
42E ILE* 1.3 96.8 - - + +
44E PHE* 1.3 66.9 + - - +
45E PRO 3.5 0.7 - - - -
46E ILE* 3.2 11.0 - - + +
47E LEU* 2.9 24.1 + - - +
119E THR* 3.5 23.1 - - - +
123E TYR* 4.0 37.4 - - + -
138E ALA* 5.5 5.2 - - + -
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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