Contacts of the helix formed by residues 40 - 52 (chain A) in PDB entry 3RQ5
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A SER 3.3 10.8 - - - +
37A ASP 3.7 3.4 - - - +
38A ASP 3.5 8.5 - - - +
39A MET* 1.3 90.8 - - - +
41A GLY* 1.3 67.3 + - - +
42A ALA 3.1 1.0 + - - -
43A ALA* 3.1 20.3 + - - +
44A LEU* 4.0 2.6 + - - +
66A VAL* 3.8 17.9 - - + +
69A LEU* 4.0 20.9 - - + -
278A GOL 3.4 22.0 - - - +
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET 3.5 1.2 - - - -
40A PRO* 1.3 84.3 - - - +
42A ALA* 1.3 63.2 + - - +
44A LEU* 3.0 10.8 + - - +
45A LEU* 3.0 31.1 + - - +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA* 4.9 0.2 - - - -
39A MET* 4.0 2.6 + - + +
40A PRO 3.1 0.8 + - - -
41A GLY* 1.3 77.6 - - - +
43A ALA* 1.3 56.1 + - - +
45A LEU* 3.8 1.6 - - - +
46A ALA* 2.9 32.9 + - - +
103A PRO* 3.6 6.6 - - + +
104A GLY* 3.3 37.9 - - - +
216A ASP* 3.4 33.2 + - - +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.8 5.1 - - - +
34A ALA* 3.6 35.2 - - + +
35A GLY* 3.7 8.2 - - - -
40A PRO 3.1 11.9 + - - +
41A GLY 3.1 0.6 - - - -
42A ALA* 1.3 77.2 - - - +
44A LEU* 1.3 59.6 + - - +
47A GLY* 2.9 25.6 + - - -
60A ILE* 4.5 5.3 - - + +
62A THR* 4.0 5.2 - - - +
66A VAL* 4.2 0.7 - - + -
70A ILE* 3.8 23.5 - - + +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PRO 4.0 1.7 + - - +
41A GLY* 3.0 14.0 + - - +
43A ALA* 1.3 76.6 - - - +
45A LEU* 1.3 61.5 + - + +
47A GLY* 3.3 0.6 + - - -
48A LEU* 2.9 52.7 + - + +
69A LEU 4.1 12.8 - - - +
70A ILE* 4.2 32.3 - - + +
73A VAL* 3.8 37.9 - - + -
74A LEU* 4.2 4.3 - - + -
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLY* 3.0 20.7 + - - +
44A LEU* 1.3 78.3 - - + +
46A ALA* 1.3 57.4 + - - +
48A LEU* 3.8 5.5 - - + +
49A GLY* 3.0 22.9 + - - -
213A GLY* 3.6 31.4 - - - +
216A ASP* 3.7 23.3 - - + +
217A THR* 3.8 19.9 + - - +
261A ALA* 4.0 2.7 - - + -
262A HIS* 3.6 44.9 - - + +
265A SER* 4.6 1.0 + - - -
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.7 28.9 - - + -
42A ALA 2.9 17.7 + - - +
43A ALA* 4.8 0.4 - - - -
45A LEU* 1.3 77.3 - - - +
47A GLY* 1.3 57.8 + - - +
50A ALA* 2.9 27.5 + - - +
103A PRO* 4.5 11.4 - - + -
216A ASP 3.3 21.7 + - - +
219A THR 5.0 0.2 - - - -
220A GLY* 3.2 16.3 - - - +
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.4 11.6 - - - +
43A ALA 2.9 19.7 + - - -
44A LEU 3.7 0.4 - - - -
45A LEU 3.3 0.2 - - - -
46A ALA* 1.3 77.6 - - - +
48A LEU* 1.3 55.1 + - - +
50A ALA* 3.3 1.6 + - - +
51A MET* 3.0 34.7 + - - +
58A LEU* 3.8 11.9 - - - -
60A ILE* 4.4 1.6 - - - -
74A LEU* 3.4 13.2 - - - -
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 2.9 44.2 + - + +
45A LEU* 3.8 5.2 - - + +
47A GLY* 1.3 70.6 - - - +
49A GLY* 1.3 67.3 + - - +
51A MET* 3.4 0.7 + - - +
52A ARG* 2.9 37.2 + - + +
73A VAL* 4.2 24.5 - - + +
74A LEU* 3.8 24.2 - - + +
262A HIS* 4.3 25.1 - - + +
265A SER* 4.0 15.9 - - - +
266A ASP* 5.8 4.3 - - - +
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU 3.0 15.3 + - - -
46A ALA 3.8 2.7 - - - -
48A LEU* 1.3 77.5 - - - +
50A ALA* 1.3 58.6 + - - +
52A ARG* 3.6 3.2 + - - +
53A SER* 2.8 30.3 + - - -
217A THR 4.1 3.8 - - - -
220A GLY 3.5 6.5 - - - -
221A MET* 3.7 18.2 - - - +
265A SER* 3.7 13.4 + - - -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 5.5 0.4 - - + -
46A ALA 2.9 16.6 + - - +
47A GLY* 3.7 4.0 - - - +
49A GLY* 1.3 76.1 - - - +
51A MET* 1.3 58.8 + - - +
53A SER* 2.9 19.6 + - - -
55A LEU* 3.4 30.5 - - + +
58A LEU* 4.3 8.7 - - + -
220A GLY 3.0 20.5 + - - +
223A LEU* 4.0 18.8 - - + -
224A GLY* 3.6 5.8 - - - +
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Residues in contact with MET 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLY 3.0 20.7 + - - +
48A LEU 4.3 0.7 - - - +
50A ALA* 1.3 76.0 - - - +
52A ARG* 1.3 61.5 + - - +
53A SER 3.3 0.2 + - - -
54A GLY* 4.1 5.5 + - - -
55A LEU* 4.0 29.5 + - + +
56A GLY 5.3 2.0 - - - +
57A LYS* 4.8 3.4 - - - -
58A LEU* 3.6 27.8 - - + +
74A LEU* 3.8 21.1 - - + -
76A GLU* 3.7 31.2 - - + +
77A ALA* 3.6 28.9 - - - -
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Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 2.9 29.6 + - + +
49A GLY* 3.8 6.5 - - - +
51A MET* 1.3 76.2 - - - +
53A SER* 1.3 58.6 + - - +
54A GLY 3.5 3.3 + - - -
265A SER* 3.1 32.6 + - - +
266A ASP* 4.4 18.8 + - - +
268A LEU* 3.9 20.5 - - + +
269A PRO* 3.7 28.5 - - - +
272A TRP* 4.1 7.1 - - - -
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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