Contacts of the helix formed by residues 39 - 58 (chain A) in PDB entry 2CRX
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 GLU 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PHE 3.8 1.8 + - - -
38A SER* 1.3 70.9 - - - +
40A HIS* 1.3 64.1 + - + +
42A TRP* 3.1 11.3 + - + +
43A LYS* 2.9 53.4 + - + +
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Residues in contact with HIS 40 (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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38A SER* 3.9 11.6 - - - -
39A GLU* 1.3 80.4 - - - +
41A THR* 1.3 64.9 + - - +
43A LYS* 3.1 8.8 + - - +
44A MET* 3.1 25.8 + - + +
11D T 5.8 2.3 + - - -
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Residues in contact with THR 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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37A PHE* 4.4 19.5 - - + -
38A SER* 2.8 33.4 + - - -
40A HIS* 1.3 74.2 - - - +
42A TRP* 1.3 61.8 + - - +
44A MET* 3.4 9.5 + - - +
45A LEU* 3.1 18.2 + - - +
94A GLN* 3.7 13.5 + - - +
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Residues in contact with TRP 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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30A MET* 4.0 30.3 - - + -
31A PHE* 5.5 1.3 - - - -
34A ARG* 2.8 52.0 + - + +
37A PHE* 3.6 31.8 - + + +
38A SER 3.0 23.6 + - - -
39A GLU* 3.3 11.4 - - + +
41A THR* 1.3 74.4 - - - +
43A LYS* 1.3 70.0 + - - +
45A LEU* 2.7 52.8 + - + +
46A LEU* 2.7 33.0 + - + +
97A MET* 5.3 2.7 - - + -
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Residues in contact with LYS 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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39A GLU* 2.9 47.8 + - + +
40A HIS* 3.5 10.1 - - - +
42A TRP* 1.3 94.4 - - - +
44A MET* 1.3 53.9 + - - +
46A LEU* 3.7 27.0 - - + +
47A SER* 2.7 37.1 + - - -
50A ARG* 4.7 3.1 + - - +
10D G 5.7 5.2 - - - +
11D T 4.3 16.7 - - + +
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Residues in contact with MET 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 HIS* 3.1 15.8 + - + +
41A THR* 3.5 11.2 - - + +
43A LYS* 1.3 75.8 - - - +
45A LEU* 1.3 57.9 + - - +
47A SER* 3.2 7.9 - - - +
48A VAL* 2.9 34.6 + - + +
90A GLN* 3.3 33.1 + - + +
94A GLN* 3.6 6.1 - - - +
11D T 3.8 26.7 - - + +
12D A 3.3 45.3 - - - +
13D T 3.7 11.7 - - + +
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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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30A MET* 6.1 2.0 - - - -
41A THR 3.1 12.2 + - - +
42A TRP* 2.7 42.0 + - + +
44A MET* 1.3 72.7 - - - +
46A LEU* 1.3 71.9 + - + +
47A SER 2.9 1.1 - - - -
48A VAL* 2.9 12.0 + - - +
49A CYS* 2.9 27.7 + - - -
94A GLN* 3.4 29.8 + - + +
97A MET* 4.3 18.2 - - + -
98A LEU* 3.3 35.9 - - + -
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Residues in contact with LEU 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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42A TRP* 2.7 38.6 + - + +
43A LYS* 3.8 35.0 - - + +
45A LEU* 1.3 76.7 - - + +
47A SER* 1.3 57.9 + - - +
49A CYS* 3.7 8.0 - - - +
50A ARG* 2.8 53.7 + - - +
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Residues in contact with SER 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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43A LYS 2.7 20.0 + - - -
44A MET* 3.2 17.0 - - - +
45A LEU 2.9 0.2 - - - -
46A LEU* 1.3 78.6 - - - +
48A VAL* 1.3 57.1 + - - +
50A ARG* 3.3 9.5 - - - +
51A SER* 3.1 28.2 + - - -
91A HIS* 5.9 0.2 - - - -
11D T 3.1 54.7 + - - +
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Residues in contact with VAL 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 MET* 2.9 19.8 + - + +
45A LEU 2.9 6.9 + - - +
47A SER* 1.3 73.1 - - - +
49A CYS* 1.3 62.0 + - - +
51A SER* 3.3 5.4 + - - -
52A TRP* 2.8 30.4 + - + +
74A TYR* 4.9 0.2 - - - +
90A GLN* 3.2 28.9 - - + +
91A HIS* 3.8 43.1 - - + +
94A GLN* 3.5 17.7 - - + -
95A LEU* 3.8 18.8 - - + -
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Residues in contact with CYS 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* 2.9 44.7 + - - +
46A LEU* 3.7 8.1 - - - +
48A VAL* 1.3 77.2 - - - +
50A ARG* 1.3 58.2 + - - +
52A TRP* 4.3 7.2 - - - -
53A ALA* 2.9 34.3 + - - +
63A TRP* 4.2 19.1 - - + -
95A LEU* 5.2 3.6 - - - -
98A LEU* 4.3 20.6 - - - -
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Residues in contact with ARG 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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43A LYS* 4.7 3.2 + - - +
46A LEU* 2.8 36.7 + - + +
47A SER* 3.3 17.9 - - - +
49A CYS* 1.3 77.5 - - - +
51A SER* 1.3 62.7 - - - +
53A ALA* 3.7 3.1 - - - +
54A ALA* 3.1 24.1 + - - +
10D G 3.8 36.9 + - - +
11D T 3.0 33.4 + - - +
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Residues in contact with SER 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 SER 3.1 12.4 + - - -
48A VAL 3.4 1.9 + - - -
50A ARG* 1.3 76.0 - - - +
52A TRP* 1.3 68.3 + - - +
54A ALA* 3.5 7.2 + - - +
55A TRP* 3.1 19.1 + - - +
74A TYR* 2.4 32.9 + - - -
78A LEU* 5.5 0.3 - - - +
81A ARG* 5.3 6.7 + - - -
91A HIS* 3.3 16.7 - - - -
11D T 5.3 11.6 + - - -
12D A 5.9 0.2 - - - -
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Residues in contact with TRP 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 VAL 2.8 19.3 + - - +
49A CYS* 3.9 1.6 - - - +
51A SER* 1.3 73.9 + - - +
53A ALA* 1.3 70.5 + - - +
55A TRP* 2.7 27.8 + + - +
56A CYS* 2.8 32.5 + - - +
62A LYS 4.3 0.7 - - - -
63A TRP* 2.9 53.8 + + + +
66A ALA* 3.3 26.9 - - + +
70A ASP* 4.1 10.3 - - + -
71A VAL* 3.7 28.0 - - + -
74A TYR* 3.5 60.8 - + + +
95A LEU* 4.1 24.5 - - + +
99A HIS* 5.7 0.6 - - - -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A CYS 2.9 22.9 + - - +
50A ARG* 3.7 4.9 - - - +
52A TRP* 1.3 77.6 - - - +
54A ALA* 1.3 57.1 + - - +
56A CYS* 3.0 11.0 + - - +
57A LYS* 2.9 29.0 + - - +
63A TRP* 4.2 23.5 - - + +
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Residues in contact with ALA 54 (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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50A ARG 3.1 15.9 + - - +
51A SER* 3.6 7.6 - - - +
53A ALA* 1.3 78.7 - - - +
55A TRP* 1.3 62.6 + - - +
57A LYS* 3.1 28.8 + - - +
58A LEU* 2.9 23.8 + - - +
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Residues in contact with TRP 55 (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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51A SER 3.1 9.6 + - - +
52A TRP* 2.7 36.5 + + - +
54A ALA* 1.3 74.4 - - - +
56A CYS* 1.3 71.7 + - - +
58A LEU* 3.5 6.2 + - + -
59A ASN* 3.0 51.2 + - - +
61A ARG* 3.4 48.9 - - + -
70A ASP 3.3 26.0 - - - -
73A ASP* 3.8 17.0 - - + -
74A TYR* 3.7 23.3 - + + -
77A TYR* 3.8 48.5 - + + +
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Residues in contact with CYS 56 (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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52A TRP* 2.8 59.0 + - - -
53A ALA 3.2 9.6 - - - +
55A TRP* 1.3 85.5 - - - +
57A LYS* 1.3 59.5 + - - +
59A ASN 3.2 1.7 + - - -
60A ASN 2.8 25.8 + - - -
61A ARG* 3.0 29.3 + - - +
62A LYS 4.3 1.6 - - - -
63A TRP* 3.4 21.8 - - + -
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Residues in contact with LYS 57 (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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53A ALA 2.9 12.0 + - - +
54A ALA* 3.4 37.2 + - - +
56A CYS* 1.3 74.3 - - - +
58A LEU* 1.3 81.2 + - + +
60A ASN* 3.1 20.7 + - - +
61A ARG 5.3 0.2 - - - -
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Residues in contact with LEU 58 (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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54A ALA 2.9 16.4 + - - +
55A TRP* 3.7 6.5 - - + +
57A LYS* 1.3 89.2 - - + +
59A ASN* 1.3 73.3 + - - +
60A ASN* 3.8 4.3 + - - -
77A TYR* 5.8 7.2 - - + +
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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