Contacts of the helix formed by residues 37 - 51 (chain D) in PDB entry 2ISZ
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D GLN* 1.3 73.7 - - - +
38D GLY* 1.3 66.9 + - - +
39D PRO* 3.9 1.6 - - - -
40D THR* 2.6 36.7 + - - -
41D VAL* 3.0 18.1 + - - +
2001D NA 4.5 0.2 - - - -
24F C 2.9 15.9 + - - -
25F T 3.3 41.0 - - - +
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Residues in contact with GLY 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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27D ARG* 5.8 0.5 - - - +
31D ALA* 4.7 6.3 - - - +
36D GLN 4.0 0.6 + - - -
37D SER* 1.3 72.3 - - - +
39D PRO* 1.3 65.7 - - - +
41D VAL* 3.2 7.7 + - - +
42D SER* 2.9 30.5 + - - -
5E G 5.4 6.1 - - - -
6E T 3.9 13.0 - - - -
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Residues in contact with PRO 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D SER* 3.5 9.9 - - - +
38D GLY* 1.3 86.0 - - - +
40D THR* 1.3 65.4 + - - +
42D SER* 3.3 4.8 + - - -
43D GLN* 2.9 29.5 + - + +
6E T 3.7 17.5 - - + +
7E T 3.5 26.5 - - + +
8E A 4.2 2.5 - - - +
24F C 3.9 12.6 - - - +
25F T 3.3 30.7 - - + +
26F A 3.6 8.5 - - - +
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Residues in contact with THR 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLN* 3.7 19.1 - - - +
37D SER* 2.6 18.5 + - - -
39D PRO* 1.3 78.4 - - - +
41D VAL* 1.3 58.5 + - - +
43D GLN* 3.2 4.9 + - - +
44D THR* 2.9 39.3 + - - +
22F T 4.9 1.6 - - + -
23F G 3.8 33.6 - - + +
24F C 2.4 44.8 + - - +
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Residues in contact with VAL 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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11D TYR* 3.2 25.3 - - + +
27D ARG* 3.5 41.1 - - + +
30D ILE* 4.2 8.5 - - + -
31D ALA* 3.7 30.3 - - + -
36D GLN* 4.5 5.8 - - + -
37D SER 3.0 18.1 + - - +
38D GLY* 3.8 4.7 - - - +
40D THR* 1.3 75.7 - - - +
42D SER* 1.3 58.2 + - - +
45D VAL* 2.8 41.6 + - + +
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Residues in contact with SER 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ARG* 3.8 21.9 + - - +
38D GLY 2.9 17.5 + - - -
39D PRO* 3.6 9.0 - - - -
41D VAL* 1.3 79.3 - - - +
43D GLN* 1.3 59.4 + - - +
45D VAL* 3.9 2.6 - - - +
46D SER* 2.8 24.1 + - - -
5E G 4.1 6.6 - - - +
6E T 2.5 31.9 + - - +
7E T 5.5 5.2 - - - -
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Residues in contact with GLN 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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39D PRO* 2.9 19.4 + - + +
40D THR* 3.6 5.4 - - - +
42D SER* 1.3 73.4 - - - +
44D THR* 1.3 65.5 + - - +
46D SER* 2.9 19.6 + - - -
47D ARG* 3.2 33.7 + - - +
7E T 5.9 5.7 - - + +
22F T 4.7 11.9 - - + +
23F G 5.8 6.5 - - - +
24F C 5.6 5.8 - - - +
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Residues in contact with THR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D THR* 3.7 26.0 - - + +
8D THR* 5.4 1.6 - - - +
11D TYR* 3.6 33.1 + - + -
40D THR* 2.9 25.7 + - - +
43D GLN* 1.3 76.8 - - - +
45D VAL* 1.3 62.3 + - - +
47D ARG* 3.1 32.6 + - - +
48D MET* 3.2 29.2 + - + +
22F T 4.5 4.3 - - - +
23F G 5.1 0.3 + - - -
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Residues in contact with VAL 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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11D TYR* 4.2 13.9 - - + -
27D ARG* 3.8 26.0 - - + +
30D ILE* 4.4 0.4 - - + -
41D VAL* 2.8 30.4 + - + +
42D SER 3.9 4.3 - - - +
44D THR* 1.3 76.1 - - - +
46D SER* 1.3 58.0 + - - +
48D MET* 3.2 9.3 + - - +
49D GLU* 2.8 26.2 + - - +
54D LEU* 3.6 15.1 - - + +
56D VAL* 3.8 28.7 - - + -
62D LEU* 4.0 18.6 - - + -
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Residues in contact with SER 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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42D SER 2.8 17.3 + - - -
43D GLN* 2.9 19.6 + - - -
45D VAL* 1.3 75.7 - - - +
47D ARG* 1.3 59.2 + - - +
49D GLU* 3.7 14.6 - - - +
50D ARG* 2.8 29.6 + - - +
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Residues in contact with ARG 47 (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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43D GLN* 3.2 30.6 + - - +
44D THR* 3.1 39.3 + - + +
46D SER* 1.3 76.1 - - - +
48D MET* 1.3 59.7 + - + +
50D ARG* 3.1 23.4 - - - +
51D ASP* 2.8 34.9 + - - +
21F G 3.5 42.3 - - - +
22F T 2.6 69.9 + - - +
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Residues in contact with MET 48 (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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8D THR* 4.0 19.5 - - + +
11D TYR* 3.6 42.2 - - + -
12D LEU* 3.7 34.5 - - + +
44D THR* 3.2 23.1 - - + +
45D VAL* 3.2 6.8 + - - +
47D ARG* 1.3 76.8 - - + +
49D GLU* 1.3 60.0 + - - +
51D ASP* 3.2 1.7 + - - +
52D GLY 3.0 4.9 + - - -
53D LEU* 2.7 53.7 + - + +
54D LEU* 3.7 21.1 - - + -
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Residues in contact with GLU 49 (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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45D VAL 2.8 15.4 + - - +
46D SER* 3.7 13.9 - - - +
48D MET* 1.3 75.8 - - - +
50D ARG* 1.3 63.1 + - - +
52D GLY* 2.9 15.6 + - - -
54D LEU* 3.3 28.0 - - + +
55D ARG* 4.5 2.4 - - - +
56D VAL* 3.5 39.5 + - - +
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Residues in contact with ARG 50 (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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46D SER 2.8 22.8 + - - +
47D ARG* 3.1 25.1 + - - +
49D GLU* 1.3 73.7 - - - +
51D ASP* 1.3 87.7 + - - +
52D GLY 3.2 3.8 + - - -
20F T 4.7 1.6 + - - -
21F G 2.8 43.0 + - - -
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Residues in contact with ASP 51 (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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47D ARG* 2.8 23.9 + - - +
48D MET* 3.2 4.6 + - - +
50D ARG* 1.3 111.6 + - - +
52D GLY* 1.3 61.9 + - - +
53D LEU* 3.3 17.0 + - + +
67D LYS* 3.3 23.8 + - - +
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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