Contacts of the helix formed by residues 38 - 61 (chain A) in PDB entry 2L35
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLY* 5.9 3.1 - - - -
32A ARG 6.0 0.2 - - - +
33A LEU* 5.4 11.7 - - + +
34A GLY 5.5 0.9 - - - +
35A THR* 3.6 17.7 - - - +
36A ALA* 2.7 22.5 + - - +
37A GLU* 1.3 72.6 - - - +
39A LEU* 1.3 68.0 + - - +
40A GLY 2.7 8.2 + - - -
41A ILE* 2.8 27.1 + - + +
42A ILE* 3.2 17.6 - - + +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU* 3.0 5.1 - - - +
38A VAL* 1.3 83.3 - - + +
40A GLY* 1.3 62.7 + - - +
42A ILE* 3.0 27.1 + - + +
43A SER* 2.9 23.9 + - - +
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU 3.0 10.5 + - - -
38A VAL 2.7 4.2 + - - -
39A LEU* 1.3 77.7 - - - +
41A ILE* 1.3 63.1 + - - -
43A SER* 3.0 19.2 + - - -
44A ILE* 3.1 19.2 + - - +
26B ALA* 5.8 2.5 - - - -
29B PHE* 5.7 6.1 - - - -
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Residues in contact with ILE 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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24A ALA* 4.7 14.6 - - + +
27A VAL* 4.1 23.6 - - + -
28A TYR* 4.9 18.6 - - + +
37A GLU 4.5 1.8 - - - +
38A VAL* 2.8 33.5 + - + +
40A GLY* 1.3 74.7 - - - -
42A ILE* 1.3 66.2 + - + +
44A ILE* 2.8 33.1 - - + +
45A VAL* 3.1 20.1 + - + +
26B ALA* 5.7 8.5 - - + +
29B PHE* 6.0 5.2 - - + -
30B LEU* 6.1 8.7 - - + -
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Residues in contact with ILE 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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28A TYR* 6.4 2.2 - - + -
38A VAL* 3.2 30.3 - - + +
39A LEU* 3.0 24.7 + - + +
41A ILE* 1.3 86.9 - - + +
43A SER* 1.3 57.4 + - - +
45A VAL* 3.3 6.7 + - - +
46A LEU* 2.9 39.0 + - + +
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Residues in contact with SER 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 LEU* 2.9 13.8 + - - +
40A GLY* 3.3 13.5 - - - -
42A ILE* 1.3 78.8 - - - +
44A ILE* 1.3 64.6 + - - +
46A LEU* 3.1 15.9 + - - +
47A VAL* 3.1 15.4 + - - +
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Residues in contact with ILE 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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20A THR* 5.0 2.0 - - + +
24A ALA* 5.6 4.0 - - + -
27A VAL* 5.7 2.7 - - + -
40A GLY 3.4 7.9 - - - +
41A ILE* 2.8 38.6 - - + +
43A SER* 1.3 76.3 - - - +
45A VAL* 1.3 65.2 + - + +
47A VAL* 3.4 10.9 - - - +
48A ALA* 3.1 24.7 + - - +
19B LEU* 4.3 2.0 - - + +
22B LEU* 3.7 34.1 - - + +
23B ILE* 4.3 29.4 - - + -
26B ALA* 3.9 28.9 - - + -
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Residues in contact with VAL 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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20A THR* 4.8 8.9 - - + +
24A ALA* 4.1 25.4 - - + -
41A ILE* 3.1 25.6 + - + +
42A ILE* 3.6 7.6 - - - +
43A SER 3.3 0.2 - - - -
44A ILE* 1.3 79.4 - - + +
46A LEU* 1.3 58.1 + - + +
48A ALA* 3.8 5.0 - - - +
49A THR* 2.6 46.1 + - - +
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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 ILE* 2.9 23.1 + - + +
43A SER* 3.1 12.3 + - - +
45A VAL* 1.3 79.2 - - + +
47A VAL* 1.3 62.0 + - - +
49A THR* 4.1 2.9 - - - -
50A VAL* 2.9 49.8 + - + +
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Residues in contact with VAL 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 SER 3.1 11.8 + - - +
44A ILE* 3.4 17.5 - - - +
46A LEU* 1.3 76.5 - - - +
48A ALA* 1.3 61.9 + - - +
50A VAL* 3.2 10.4 - - + +
51A LEU* 2.9 37.7 + - + +
19B LEU* 3.9 16.2 - - + -
22B LEU* 4.3 14.4 - - + -
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Residues in contact with ALA 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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20A THR* 3.8 21.8 - - + +
44A ILE 3.1 14.5 + - - +
45A VAL 3.8 3.1 - - - +
47A VAL* 1.3 79.2 - - - +
49A THR* 1.3 66.8 + - - +
51A LEU* 3.2 1.9 + - - -
52A LYS* 3.1 34.6 + - - +
19B LEU* 3.5 35.9 - - + -
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Residues in contact with THR 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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17A LEU* 5.9 10.3 - - + +
45A VAL* 2.6 31.7 + - - +
46A LEU* 4.1 4.3 - - - -
48A ALA* 1.3 77.8 - - - +
50A VAL* 1.3 60.0 + - + +
52A LYS* 4.3 3.7 - - - +
53A THR* 2.4 46.0 + - - +
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Residues in contact with VAL 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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46A LEU* 2.9 44.0 - - + +
47A VAL* 3.2 18.4 - - + +
49A THR* 1.3 78.1 - - + +
51A LEU* 1.3 64.4 + - + +
53A THR* 4.2 4.7 - - - -
54A ILE* 2.8 53.1 + - + +
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Residues in contact with LEU 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 VAL* 2.9 26.9 + - + +
48A ALA 3.2 4.7 + - - +
50A VAL* 1.3 77.4 - - - +
52A LYS* 1.3 68.0 + - + +
54A ILE* 5.0 0.7 - - - -
55A VAL* 2.9 53.5 + - + +
12B ILE* 6.2 0.9 - - + -
15B GLY* 3.9 31.9 - - - +
18B VAL* 5.7 4.7 - - + -
19B LEU* 5.2 7.4 - - + -
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Residues in contact with LYS 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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13A VAL* 5.5 8.1 - - + +
16A ASP* 2.5 63.5 + - + +
17A LEU* 3.5 19.3 - - + +
20A THR* 4.0 3.3 + - - -
48A ALA* 3.1 37.0 + - - +
49A THR* 4.4 2.9 - - - +
51A LEU* 1.3 86.5 - - + +
53A THR* 1.3 55.2 + - - +
55A VAL* 4.0 5.6 - - - -
56A LEU* 2.7 42.3 + - + +
12B ILE* 4.2 20.9 - - + +
15B GLY* 5.6 0.9 - - - -
19B LEU* 3.9 14.4 - - + -
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Residues in contact with THR 53 (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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49A THR* 2.4 37.1 + - + +
50A VAL* 4.1 4.0 - - - -
52A LYS* 1.3 80.1 - - - +
54A ILE* 1.3 60.6 + - + +
56A LEU* 4.8 1.3 - - - -
57A ILE* 3.1 57.8 + - + +
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Residues in contact with ILE 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 VAL* 2.8 50.2 + - + +
51A LEU* 4.3 1.3 - - - +
53A THR* 1.3 75.5 - - + +
55A VAL* 1.3 59.0 + - + +
58A PRO* 2.6 39.4 - - + +
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Residues in contact with VAL 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 LEU* 2.9 43.9 + - + +
52A LYS 3.6 0.9 - - - +
54A ILE* 1.3 83.7 - - + +
56A LEU* 1.3 65.8 + - - +
58A PRO* 4.2 2.9 - - - +
59A PHE* 3.8 18.9 + - - +
8B VAL* 4.1 15.2 - - + +
11B GLY 5.9 2.0 - - - -
12B ILE* 3.4 29.2 - - + -
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Residues in contact with LEU 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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13A VAL* 3.8 42.6 - - + -
52A LYS* 2.7 24.8 + - + +
53A THR* 4.5 1.6 - - - +
55A VAL* 1.3 81.3 - - + +
57A ILE* 1.3 61.8 + - + +
59A PHE 3.4 0.2 + - - -
60A LEU* 2.8 64.8 + - + +
8B VAL* 5.9 2.0 - - + -
9B LEU* 4.1 6.7 - - + -
12B ILE* 4.0 17.3 - - + -
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Residues in contact with ILE 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 THR* 3.1 43.2 + - + +
56A LEU* 1.3 75.1 - - + +
58A PRO* 1.3 63.8 - - + +
59A PHE 2.7 4.2 + - - -
60A LEU* 4.9 2.0 - - - -
61A GLU* 2.5 63.5 + - + +
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Residues in contact with PRO 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 ILE* 2.6 34.5 - - + +
55A VAL* 4.2 5.6 - - - +
57A ILE* 1.3 97.7 - - + +
59A PHE* 1.3 60.9 + - + +
61A GLU* 3.9 17.0 - - + +
63A ASN* 5.3 4.9 + - - -
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Residues in contact with PHE 59 (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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55A VAL 3.8 15.5 - - - +
56A LEU 3.4 2.1 + - - +
57A ILE 2.7 5.1 + - - -
58A PRO* 1.3 76.3 - - - +
60A LEU* 1.3 67.3 + - + +
61A GLU 2.8 19.4 + - - +
4B VAL* 3.6 44.2 - - + -
8B VAL* 3.4 39.3 - - + -
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Residues in contact with LEU 60 (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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4A VAL* 4.6 21.5 - - + -
56A LEU* 2.8 52.6 + - + +
57A ILE* 4.9 1.6 - - - -
59A PHE* 1.3 84.7 - - + +
61A GLU* 1.3 60.2 + - - +
62A GLN* 3.7 12.7 + - - +
8B VAL* 5.1 1.3 - - + -
9B LEU* 4.1 18.2 - - + -
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Residues in contact with GLU 61 (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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57A ILE* 2.5 44.9 + - + +
58A PRO* 3.9 12.5 - - - +
59A PHE 2.8 13.2 + - - +
60A LEU* 1.3 74.6 - - - +
62A GLN* 1.3 65.0 + - + +
63A ASN* 2.7 27.4 + - - -
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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