Contacts of the helix formed by residues 37 - 51 (chain A) in PDB entry 2IT0
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 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN* 1.3 72.9 - - - +
38A GLY* 1.3 63.8 + - - +
39A PRO* 3.6 3.4 - - - +
40A THR* 2.8 34.5 + - - -
41A VAL* 3.0 17.8 + - - +
19F C 2.9 15.6 + - - -
20F T 3.5 38.8 - - - +
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Residues in contact with GLY 38 (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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27A ARG* 5.8 0.3 - - - +
31A ALA* 4.5 9.4 - - - +
36A GLN 3.7 1.0 + - - -
37A SER* 1.3 69.7 - - - +
39A PRO* 1.3 65.1 - - - +
41A VAL* 3.2 11.4 + - - +
42A SER* 2.9 30.8 + - - -
10E C 6.3 2.9 - - - -
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Residues in contact with PRO 39 (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 SER* 3.5 10.5 - - - +
38A GLY* 1.3 90.1 - - - +
40A THR* 1.3 61.1 + - - +
42A SER* 3.7 7.2 - - - -
43A GLN* 3.0 25.1 + - - +
10E C 6.6 0.2 - - + -
11E A 4.8 4.5 - - - +
12E C 3.5 28.5 - - + +
13E A 4.4 2.5 - - - +
19F C 4.3 10.1 + - - +
20F T 3.3 31.6 - - + +
21F G 3.9 5.8 - - - +
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 4.3 2.2 - - - +
36A GLN* 4.0 14.8 - - - +
37A SER* 2.8 20.8 + - - -
39A PRO* 1.3 77.7 - - - +
41A VAL* 1.3 63.5 + - - +
43A GLN* 3.3 5.6 + - - +
44A THR* 3.0 28.5 + - - +
17F G 5.1 0.7 - - + +
18F C 3.7 39.9 - - + +
19F C 2.7 41.1 + - - +
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Residues in contact with VAL 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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11A TYR* 3.1 27.1 - - + +
27A ARG* 3.6 41.1 - - + +
30A ILE* 4.6 5.2 - - + -
31A ALA* 4.0 24.9 - - + +
36A GLN* 4.4 6.5 - - + +
37A SER 3.0 21.3 - - - +
38A GLY* 3.6 6.5 - - - +
40A THR* 1.3 71.6 - - - +
42A SER* 1.3 63.0 + - - +
44A THR* 3.1 0.5 + - - -
45A VAL* 2.7 40.0 + - + +
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 3.8 22.6 + - - +
38A GLY 2.9 18.2 + - - -
39A PRO* 3.7 8.5 - - - -
41A VAL* 1.3 81.5 - - - +
43A GLN* 1.3 64.1 + - - +
45A VAL* 3.2 2.6 + - - +
46A SER* 3.0 26.6 + - - -
10E C 6.3 0.2 - - - -
11E A 2.8 28.9 + - - -
12E C 6.5 0.7 - - - -
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Residues in contact with GLN 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 PRO 3.0 19.3 + - - +
40A THR* 3.7 5.2 - - - +
42A SER* 1.3 76.9 - - - +
44A THR* 1.3 61.9 + - - +
46A SER* 3.5 8.2 - - - -
47A ARG* 3.2 29.5 + - + +
43C GLN* 5.4 6.5 + - - +
14E G 5.3 4.4 + - - -
15E G 5.3 1.2 + - - -
17F G 3.7 22.2 + - - +
18F C 3.4 33.6 + - - +
19F C 5.2 2.4 + - - +
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Residues in contact with THR 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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7A THR* 3.8 15.1 - - + +
8A THR* 5.4 1.6 - - - +
11A TYR* 3.4 36.7 + - + -
40A THR* 3.0 19.6 + - - +
41A VAL 3.1 0.2 + - - -
43A GLN* 1.3 74.9 + - - +
45A VAL* 1.3 60.3 + - - +
47A ARG* 3.1 37.6 + - - +
48A MET* 3.1 32.0 + - + +
17F G 4.0 12.7 - - - +
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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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11A TYR* 3.9 21.1 - - + -
27A ARG* 4.0 23.8 - - + +
30A ILE* 4.7 2.2 - - + -
41A VAL* 2.7 22.3 + - + +
42A SER 3.7 4.0 - - - +
44A THR* 1.3 75.1 - - - +
46A SER* 1.3 58.6 + - - +
48A MET* 3.2 9.3 + - - +
49A GLU* 2.8 26.7 + - - +
54A LEU* 3.8 15.9 - - + +
56A VAL* 3.8 28.0 - - + -
62A LEU* 4.2 17.3 - - + -
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Residues in contact with SER 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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27A ARG* 5.8 1.4 + - - -
42A SER* 3.0 14.9 + - - -
43A GLN* 3.5 12.8 - - - -
45A VAL* 1.3 77.9 - - - +
47A ARG* 1.3 58.1 + - - -
49A GLU* 3.0 12.3 + - - +
50A ARG* 2.8 31.5 + - - +
56A VAL* 6.0 0.7 - - - -
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Residues in contact with ARG 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 GLN* 3.2 18.7 + - + +
44A THR* 3.1 46.0 + - - +
45A VAL 3.2 0.2 - - - -
46A SER* 1.3 79.9 - - - +
48A MET* 1.3 58.1 + - + +
50A ARG* 3.2 23.6 + - - +
51A ASP* 3.0 35.8 + - - +
16F A 3.6 43.1 - - - +
17F G 2.8 63.7 + - - +
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Residues in contact with MET 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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8A THR* 3.8 20.2 - - + +
11A TYR* 3.6 45.1 - - + -
12A LEU* 3.6 36.1 - - + +
44A THR* 3.1 18.9 + - + +
45A VAL* 3.2 6.9 + - - +
47A ARG* 1.3 74.0 - - + +
49A GLU* 1.3 62.2 + - - +
51A ASP* 3.4 3.2 + - - +
52A GLY 3.3 2.8 + - - -
53A LEU* 2.8 51.7 + - + +
54A LEU* 3.5 22.8 + - + -
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Residues in contact with GLU 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 VAL 2.8 13.8 + - - +
46A SER* 3.0 14.0 + - - +
48A MET* 1.3 75.4 - - - +
50A ARG* 1.3 59.5 + - - +
52A GLY* 2.9 21.5 + - - -
54A LEU* 3.2 22.9 - - + +
55A ARG* 3.2 9.0 + - + +
56A VAL* 2.7 46.7 + - + +
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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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46A SER 2.8 12.5 + - - +
47A ARG* 3.3 26.9 - - - +
49A GLU* 1.3 77.5 - - - +
51A ASP* 1.3 85.4 + - - +
52A GLY 3.4 0.8 + - - -
15F C 5.5 0.4 - - - -
16F A 2.9 40.4 + - - -
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Residues in contact with ASP 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 ARG* 3.0 17.7 + - - +
48A MET* 3.4 4.4 + - - +
49A GLU 3.0 1.4 - - - -
50A ARG* 1.3 118.1 + - - +
52A GLY* 1.3 50.0 + - - +
53A LEU* 3.2 14.5 + - + +
67A LYS* 2.6 33.0 + - - +
16F A 4.7 1.6 + - - -
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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