Contacts of the helix formed by residues 31 - 53 (chain A) in PDB entry 4ZGM
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 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A THR 3.4 6.1 + - - -
30A VAL* 1.3 76.1 - - - +
32A LEU* 1.3 65.1 + - - +
33A TRP* 3.5 7.3 + - - +
34A GLU* 3.1 29.4 + - - +
35A THR* 2.9 27.3 + - - -
21B GLU* 5.0 9.6 - - - -
25B ALA* 4.0 1.3 - - - -
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Residues in contact with LEU 32 (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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31A SER* 1.3 73.7 - - - +
33A TRP* 1.3 59.5 + - - +
35A THR* 3.2 2.1 + - - -
36A VAL* 2.8 46.7 + - + +
21B GLU 4.6 3.2 + - - -
24B ALA* 3.6 33.9 - - + +
25B ALA* 4.0 11.9 - - - +
28B PHE* 3.5 33.7 - - + -
101B 32M 4.1 32.8 - - + -
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Residues in contact with TRP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 3.2 6.5 + - - +
32A LEU* 1.3 81.7 - - + +
34A GLU* 1.3 58.1 + - - +
36A VAL* 3.4 25.7 + - + -
37A GLN* 3.0 70.1 + - + +
40A ARG* 4.2 16.4 - - - -
101B 32M 5.3 8.7 - - + -
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR 5.4 0.7 - - - +
30A VAL* 3.6 28.9 - - + +
31A SER* 3.1 25.7 + - - +
33A TRP* 1.3 76.6 - - - +
35A THR* 1.3 57.9 + - - +
37A GLN* 3.4 12.9 + - - +
38A LYS* 3.1 55.1 + - + +
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Residues in contact with THR 35 (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 VAL* 3.5 17.2 - - - +
31A SER 2.9 14.6 + - - -
32A LEU 3.5 7.2 - - - -
34A GLU* 1.3 75.4 - - - +
36A VAL* 1.3 59.9 + - - +
38A LYS* 3.3 7.5 + - - +
39A TRP* 2.9 28.4 + - - +
88A TYR* 3.7 21.4 + - + +
90A PRO* 3.9 8.4 - - + +
25B ALA* 3.8 12.8 - - + +
28B PHE* 3.9 21.8 - - + -
29B ILE* 3.9 16.2 - - + -
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 2.8 42.7 + - + +
33A TRP* 3.8 23.1 - - + +
35A THR* 1.3 71.8 - - - +
37A GLN* 1.3 64.0 + - - +
39A TRP* 3.2 2.6 + - + +
40A ARG* 2.9 37.8 + - + +
28B PHE* 3.9 24.7 - - + -
101B 32M 3.9 39.3 - - + -
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Residues in contact with GLN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.0 70.3 + - + +
34A GLU* 3.8 9.7 - - - +
35A THR 3.3 0.2 - - - -
36A VAL* 1.3 76.3 - - - +
38A LYS* 1.3 63.0 + - + +
40A ARG* 3.4 17.6 + - - +
41A GLU* 3.2 21.5 + - - +
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Residues in contact with LYS 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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30A VAL* 5.9 1.5 - - + +
34A GLU* 3.1 47.0 + - + +
35A THR* 3.7 4.0 - - - +
37A GLN* 1.3 72.6 - - + +
39A TRP* 1.3 61.8 + - - +
41A GLU* 3.1 3.1 + - - -
42A TYR* 2.9 28.6 + - - +
87A TRP* 3.5 29.1 + - + +
88A TYR* 3.5 32.1 - - + +
89A LEU 5.7 2.2 + - - +
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Residues in contact with TRP 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR 2.9 17.4 + - - +
36A VAL* 3.6 3.8 - - + +
38A LYS* 1.3 77.4 - - - +
40A ARG* 1.3 77.3 + - + +
42A TYR* 3.2 1.6 + + - +
43A ARG* 2.8 74.6 + - + +
66A PHE* 3.7 12.1 - + - -
68A GLU* 2.8 40.1 + - - -
88A TYR* 3.6 31.8 - + + +
28B PHE* 4.0 23.3 - + + -
32B LEU* 3.4 22.0 - - + +
36B ARG* 3.6 24.0 - - - -
101B 32M 4.1 19.3 - - + -
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 4.2 21.1 - - - -
36A VAL* 2.9 35.2 + - + +
37A GLN* 3.6 15.6 - - - +
38A LYS 3.3 0.2 - - - -
39A TRP* 1.3 95.5 - - + +
41A GLU* 1.3 57.7 + - - +
43A ARG* 3.4 21.8 + - - +
44A ARG* 2.9 27.3 + - - +
101B 32M 6.0 2.7 - - + -
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Residues in contact with GLU 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 GLN 3.2 11.3 + - - +
38A LYS* 3.1 9.8 + - - +
40A ARG* 1.3 75.4 - - - +
42A TYR* 1.3 60.0 + - - +
44A ARG* 2.7 51.5 + - - +
45A GLN* 2.9 51.8 + - - +
87A TRP* 3.8 12.8 - - + -
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Residues in contact with TYR 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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38A LYS 2.9 14.2 + - - +
39A TRP* 3.5 7.4 - + - +
41A GLU* 1.3 75.0 - - - +
43A ARG* 1.3 59.1 + - - +
45A GLN* 3.3 4.9 + - + +
46A CYS* 2.9 25.3 + - - +
66A PHE* 4.0 15.9 - + - -
69A TYR 3.9 10.8 - - - -
70A ALA* 3.5 7.8 - - - +
71A CYS* 3.0 44.4 + - + +
83A VAL* 5.1 1.9 - - - +
84A SER 4.9 3.9 + - - -
86A PRO* 3.9 25.9 - - + +
87A TRP* 3.4 42.7 - + + +
88A TYR* 3.6 25.4 - + + -
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 2.8 53.1 + - + +
40A ARG* 3.6 21.7 + - - +
42A TYR* 1.3 74.4 - - - +
44A ARG* 1.3 56.4 + - - +
46A CYS* 3.2 6.8 + - - +
47A GLN* 2.8 55.1 + - - +
66A PHE* 3.6 36.6 - - + -
68A GLU* 5.0 1.1 + - - -
36B ARG* 4.1 16.4 - - - +
101B 32M 6.0 1.0 - - - +
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Residues in contact with ARG 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 ARG 2.9 15.5 + - - +
41A GLU* 2.7 47.1 + - - +
43A ARG* 1.3 74.8 - - - +
45A GLN* 1.3 71.6 + - - +
47A GLN* 3.3 11.7 + - - +
48A ARG* 3.1 63.2 + - - +
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Residues in contact with GLN 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 GLU* 2.9 47.8 + - - +
42A TYR* 3.7 5.4 - - - +
44A ARG* 1.3 85.5 - - - +
46A CYS* 1.3 62.9 + - - +
48A ARG* 3.3 23.1 + - - +
49A SER* 3.1 24.4 + - - -
87A TRP* 4.1 22.2 + - - -
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Residues in contact with CYS 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 TYR* 2.9 17.0 + - + +
43A ARG* 3.2 8.3 + - - +
45A GLN* 1.3 76.8 - - - +
47A GLN* 1.3 64.0 + - - +
49A SER* 3.0 5.6 + - - +
50A LEU* 2.9 33.7 + - - +
66A PHE* 3.7 28.7 - - + -
71A CYS* 2.1 57.2 - - + -
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Residues in contact with GLN 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 ARG* 2.8 53.2 + - + +
44A ARG* 3.3 9.6 + - - +
46A CYS* 1.3 74.1 - - + +
48A ARG* 1.3 61.5 + - - +
50A LEU* 3.3 17.6 + - + +
51A THR* 3.0 28.8 + - - -
66A PHE* 5.1 7.1 - - + -
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Residues in contact with ARG 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 ARG* 3.1 50.9 + - - +
45A GLN* 3.4 24.6 + - - +
46A CYS 3.2 0.2 - - - -
47A GLN* 1.3 76.5 - - - +
49A SER* 1.3 59.8 + - - +
51A THR* 3.3 4.6 + - - -
52A GLU* 2.8 59.9 + - + +
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Residues in contact with SER 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 GLN 3.1 10.2 + - - -
46A CYS* 3.0 12.2 + - - -
48A ARG* 1.3 81.6 - - - +
50A LEU* 1.3 63.4 + - - +
52A GLU* 4.9 0.9 - - - -
53A ASP* 2.8 54.4 + - - +
71A CYS* 4.8 8.9 - - - -
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Residues in contact with LEU 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 CYS* 2.9 34.3 + - - +
47A GLN* 3.3 18.8 + - + +
49A SER* 1.3 75.8 - - - +
51A THR* 1.3 59.3 + - - +
64A ARG* 2.8 62.0 + - + +
65A THR* 3.8 17.0 - - - +
66A PHE* 4.1 17.9 - - + +
71A CYS* 4.7 2.2 - - - -
72A TRP 4.3 3.8 - - - +
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Residues in contact with THR 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 GLN* 3.0 18.1 + - - +
48A ARG* 3.7 5.2 - - - -
50A LEU* 1.3 80.3 - - - +
52A GLU* 1.3 70.3 + - + +
53A ASP 3.6 3.3 - - - +
64A ARG* 4.8 0.2 + - - -
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 2.8 45.5 + - + +
49A SER* 4.9 1.1 - - - -
51A THR* 1.3 83.6 - - + +
53A ASP* 1.3 70.0 + - - +
54A PRO* 3.4 5.0 - - - +
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Residues in contact with ASP 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 SER* 2.8 43.2 + - - +
51A THR 4.4 2.4 - - - +
52A GLU* 1.3 81.0 - - - +
54A PRO* 1.3 72.9 - - + +
55A PRO* 3.7 0.7 - - - +
64A ARG* 2.9 32.9 + - - +
73A PRO* 5.7 5.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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