Contacts of the helix formed by residues 32 - 46 (chain D) in PDB entry 2CFX
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 SER 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D LEU* 1.3 77.6 - - - +
33D PRO* 1.4 74.5 - - - +
34D PRO* 4.2 5.8 - - - +
35D SER* 3.2 21.8 + - - -
36D VAL* 3.0 17.4 + - - +
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Residues in contact with PRO 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D MET* 4.7 8.7 - - + +
23D ARG* 4.5 26.7 - - + +
26D GLY* 4.7 4.7 - - - -
31D LEU 3.4 6.7 - - - +
32D SER* 1.4 89.3 - - - +
34D PRO* 1.4 71.6 - - + +
35D SER 2.8 3.6 + - - -
36D VAL* 3.1 14.7 + - + +
37D THR* 3.1 17.4 + - + +
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Residues in contact with PRO 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D SER* 4.4 5.2 - - - +
33D PRO* 1.4 89.3 - - + +
35D SER* 1.3 59.3 + - - +
37D THR* 3.4 17.2 + - + +
38D GLU* 3.6 18.2 + - - +
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Residues in contact with SER 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 3.4 27.9 - - - +
32D SER* 3.1 25.1 + - - -
33D PRO 2.8 4.8 + - - -
34D PRO* 1.3 71.2 - - - +
36D VAL* 1.3 64.1 + - - -
38D GLU* 3.3 15.0 + - - +
39D ARG* 3.4 16.3 + - - +
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Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 4.6 3.6 - - + -
22D MET* 3.9 23.3 - - + +
25D LEU* 3.6 34.5 - - + +
26D GLY* 4.1 15.9 - - - -
29D ILE* 4.5 12.8 - - + -
31D LEU* 3.8 25.1 - - + -
32D SER 3.0 9.4 + - - +
33D PRO* 3.3 10.3 - - + +
35D SER* 1.3 75.5 + - - +
37D THR* 1.3 61.3 + - - +
39D ARG* 3.0 27.5 + - - +
40D VAL* 3.0 12.3 + - - +
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Residues in contact with THR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D MET* 3.5 44.2 - - + -
33D PRO* 3.1 19.0 + - + +
34D PRO* 3.4 17.8 + - + +
35D SER 3.3 0.6 - - - -
36D VAL* 1.3 74.8 - - - +
38D GLU* 1.3 57.3 + - - +
40D VAL* 3.8 1.9 - - - +
41D ARG* 2.8 29.1 + - - +
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Residues in contact with GLU 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D PRO 3.6 12.4 + - - +
35D SER* 3.3 10.4 + - - +
36D VAL 3.1 0.8 - - - -
37D THR* 1.3 76.4 + - - +
39D ARG* 1.3 66.4 + - - +
41D ARG* 3.3 19.0 - - - +
42D GLN* 3.2 30.4 + - + +
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Residues in contact with ARG 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ASP* 2.8 36.2 + - - -
6D ILE* 3.6 26.2 - - - +
7D ASP* 2.8 44.9 + - - +
10D ILE* 3.2 25.6 - - + -
31D LEU* 3.9 19.9 - - - +
35D SER* 3.4 11.8 + - - +
36D VAL* 3.0 8.9 + - - +
38D GLU* 1.3 79.2 - - - +
40D VAL* 1.3 56.4 + - - +
42D GLN* 3.4 2.1 + - - +
43D LEU* 3.0 35.2 + - - +
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 4.0 15.9 - - + -
14D LEU* 4.6 6.7 - - + -
22D MET* 3.9 28.3 - - + -
25D LEU* 3.9 19.3 - - + -
36D VAL 3.0 14.2 + - - +
37D THR 4.1 3.6 - - - +
39D ARG* 1.3 72.4 - - - +
41D ARG* 1.3 68.6 + - - +
43D LEU* 4.3 6.5 - - - -
44D GLU* 3.2 29.6 + - - +
49D ILE* 4.6 4.7 - - + -
52D TYR* 3.4 24.9 - - - +
19G ARG* 6.0 0.2 - - - +
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Residues in contact with ARG 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D THR* 2.8 21.3 + - - +
38D GLU* 3.3 22.4 - - - +
39D ARG 3.2 0.8 - - - -
40D VAL* 1.3 78.9 - - - +
42D GLN* 1.3 58.1 + - - +
44D GLU* 4.1 10.0 - - - +
45D SER* 3.2 26.9 + - - -
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Residues in contact with GLN 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.2 11.6 - - + +
38D GLU* 3.2 25.1 + - + +
39D ARG* 4.3 1.8 - - - +
41D ARG* 1.3 77.2 - - - +
43D LEU* 1.4 57.7 + - - +
45D SER* 3.4 9.0 - - - +
46D PHE* 3.0 49.6 + - + -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 4.1 13.4 - - + -
3D LEU* 4.0 26.5 - - + -
7D ASP* 4.1 25.4 - - - +
10D ILE* 3.6 31.9 - - + -
11D ILE* 3.7 17.3 - - + -
39D ARG 3.0 25.0 + - - +
40D VAL* 4.0 4.5 - - - +
42D GLN* 1.4 77.2 - - - +
44D GLU* 1.3 59.3 + - - +
46D PHE* 4.0 0.7 - - - +
47D GLY 3.5 2.9 + - - -
48D ILE* 3.1 39.1 + - + +
49D ILE* 3.4 19.3 + - + -
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Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D VAL* 3.2 27.2 + - - +
41D ARG* 4.1 7.5 - - - +
43D LEU* 1.3 78.5 - - - +
45D SER* 1.3 64.1 + - - +
47D GLY* 3.6 9.9 + - - -
49D ILE* 3.8 27.1 - - + +
52D TYR* 3.1 36.3 + - - +
19G ARG* 3.6 11.7 + - - -
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ARG 3.2 16.9 + - - -
42D GLN* 3.3 15.6 + - - +
44D GLU* 1.3 75.9 - - - +
46D PHE* 1.3 69.0 + - - +
47D GLY* 3.1 6.2 + - - -
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Residues in contact with PHE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 2.9 64.8 - - + -
42D GLN* 3.0 28.7 + - + +
43D LEU 4.3 0.2 - - - +
44D GLU 3.5 0.2 - - - -
45D SER* 1.3 81.9 + - - +
47D GLY* 1.3 59.3 + - - +
48D ILE* 3.4 12.2 + - + +
60G LYS* 5.2 3.8 - - - +
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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