Contacts of the helix formed by residues 49 - 60 (chain B) in PDB entry 3F2F
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 PRO 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B ALA* 4.7 0.4 - - - -
47B ASP 4.5 1.8 - - - +
48B TRP* 1.3 94.2 - - + +
50B ALA* 1.3 65.1 + - - +
51B GLU* 3.2 19.8 + - + +
52B ARG* 3.2 25.3 + - + +
53B VAL* 3.5 9.2 + - - +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B THR* 6.2 3.8 - - + -
43B ALA* 4.8 9.5 - - + +
48B TRP 3.8 0.8 + - - -
49B PRO* 1.3 72.4 - - - +
51B GLU* 1.3 76.1 + - - +
53B VAL* 3.5 7.7 + - - +
54B ALA* 3.1 25.3 + - - +
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PRO* 3.1 14.1 - - + +
50B ALA* 1.3 97.5 + - - +
52B ARG* 1.3 57.5 + - - +
54B ALA* 3.5 5.2 + - - +
55B ALA* 2.9 28.8 + - - +
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLY* 3.5 31.4 - - - +
22B ASP* 4.3 5.1 + - - -
48B TRP* 3.3 49.6 - - + +
49B PRO* 3.2 23.1 + - + +
51B GLU* 1.3 76.4 - - - +
53B VAL* 1.3 64.5 + - - +
55B ALA* 3.3 7.0 + - + +
56B VAL* 3.2 26.6 + - + +
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 4.2 9.4 - - + -
39B ARG* 4.1 24.9 - - + +
42B LEU* 4.5 7.9 - - + -
43B ALA* 3.8 36.6 - - + +
46B LEU* 4.6 3.4 - - + -
48B TRP* 3.7 24.4 - - + -
49B PRO 3.5 5.3 + - - +
50B ALA* 3.5 8.7 + - - +
51B GLU 3.4 0.4 - - - -
52B ARG* 1.3 76.7 - - - +
54B ALA* 1.3 63.2 + - - +
56B VAL* 3.2 4.7 + - - +
57B LEU* 3.1 41.6 + - + +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ARG* 3.5 30.4 + - - +
50B ALA 3.1 17.9 + - - +
51B GLU* 3.8 5.4 - - - +
53B VAL* 1.3 77.7 - - - +
55B ALA* 1.3 58.0 + - - +
57B LEU* 3.9 1.0 - - - +
58B GLU* 3.0 31.5 + - - +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU 2.9 18.1 + - - +
52B ARG* 3.6 10.1 - - + +
53B VAL 3.2 0.2 - - - -
54B ALA* 1.3 78.1 - - - +
56B VAL* 1.3 62.6 + - + +
58B GLU* 3.6 20.9 + - - +
59B GLN* 3.8 13.7 + - - +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLY* 4.1 19.3 - - - -
20B THR* 3.9 34.2 + - + +
23B LEU* 4.0 23.1 - - + -
48B TRP* 3.9 18.2 - - + -
52B ARG* 3.2 18.6 + - + +
53B VAL 3.2 6.7 + - - +
55B ALA* 1.3 79.0 - - + +
57B LEU* 1.3 63.4 + - + +
59B GLN* 3.3 14.9 + - - +
60B ALA* 3.5 9.4 + - - +
74B TYR* 5.0 4.0 - - - +
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 4.3 16.6 - - + -
39B ARG* 3.4 54.5 - - + +
42B LEU* 4.7 1.6 - - + -
53B VAL* 3.1 23.1 + - + +
54B ALA 4.0 1.8 - - - +
56B VAL* 1.3 74.6 - - + +
58B GLU* 1.3 64.4 + - - +
60B ALA* 2.9 25.7 + - - +
63B THR* 4.4 6.8 + - + +
65B TYR* 4.0 8.7 + - - +
71B ILE* 3.8 23.6 - - + -
74B TYR* 4.0 28.3 - - + -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ARG* 5.2 1.9 - - - +
54B ALA 3.0 18.6 + - - +
55B ALA* 3.7 12.8 - - - +
56B VAL 3.2 0.6 - - - -
57B LEU* 1.3 77.8 - - - +
59B GLN* 1.3 79.5 + - - +
61B THR* 3.7 15.8 - - - +
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Residues in contact with GLN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 6.1 1.3 - - - +
55B ALA 4.0 9.4 + - - +
56B VAL* 3.3 8.1 + - - +
57B LEU 3.1 0.4 - - - -
58B GLU* 1.3 111.2 + - - +
60B ALA* 1.3 58.5 + - - +
61B THR* 3.1 16.4 + - - +
152B ALA 5.7 0.3 - - - +
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 6.3 0.2 - - + -
56B VAL 3.5 8.8 + - - +
57B LEU* 2.9 17.6 + - - +
59B GLN* 1.3 74.1 - - - +
61B THR* 1.3 59.6 + - - +
62B SER* 3.2 5.8 - - - -
63B THR* 2.7 37.8 + - - +
65B TYR* 5.3 0.3 + - - -
74B TYR* 3.8 28.7 - - + +
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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