Contacts of the helix formed by residues 40 - 54 (chain B) in PDB entry 4Z2C
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 LYS 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ARG 3.6 13.0 - - - +
31B ALA* 2.7 32.2 + - - +
32B LEU 3.9 12.8 - - - +
33B PRO* 4.0 8.9 - - + +
38B GLY 5.8 0.2 - - - +
39B LEU* 1.3 74.1 - - - +
41B PRO* 1.3 64.9 - - + -
42B VAL* 3.2 6.3 - - + +
43B HIS* 2.8 67.1 + - + +
44B ARG* 3.3 8.3 + - - -
169B ALA* 6.0 0.7 - - - -
170B THR 2.4 35.2 + - - +
171B GLY 3.5 1.0 - - - +
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Residues in contact with PRO 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL 5.4 0.2 - - - +
29B ALA* 3.5 35.4 - - + +
30B ARG* 4.0 13.2 - - + +
32B LEU 4.3 5.8 - - - +
39B LEU 4.5 1.8 - - - +
40B LYS* 1.3 87.0 - - + -
42B VAL* 1.3 56.9 + - - +
44B ARG* 3.4 19.2 + - + +
45B ARG* 2.9 61.6 + - + +
76B HIS* 4.8 3.1 - - + -
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ARG 5.4 3.1 - - - +
40B LYS* 2.9 10.2 + - + +
41B PRO* 1.3 76.6 - - - +
43B HIS* 1.3 83.7 + - + +
45B ARG* 3.8 2.2 - - - +
46B ILE* 2.9 41.2 + - + +
76B HIS* 3.8 34.1 - - + +
82B SER* 4.7 2.9 - - - +
83B ILE* 4.2 14.1 - - + +
86B ALA* 3.7 23.1 - - + -
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Residues in contact with HIS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.8 22.9 - - + -
40B LYS* 2.8 49.1 + - + +
42B VAL* 1.3 81.0 - - + +
44B ARG* 1.3 59.9 + - - +
46B ILE* 3.1 5.5 + - - +
47B LEU* 2.9 33.7 + - - +
86B ALA* 4.3 15.0 + - + +
89B ARG* 4.5 11.8 + - - -
90B MET* 3.4 32.7 - - + +
96B TYR* 3.0 29.0 + + - -
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP* 3.4 13.5 + - - +
37B ASP* 2.8 34.1 + - - -
39B LEU* 2.8 42.8 + - + +
40B LYS 3.3 3.8 + - - +
41B PRO* 3.8 24.7 - - + +
43B HIS* 1.3 77.3 - - - +
45B ARG* 1.3 60.0 + - + +
47B LEU* 3.3 1.9 + - - +
48B TYR* 2.9 30.0 + - - +
154B PRO* 3.6 19.3 - - + +
155B LEU 3.5 26.9 + - - -
156B VAL* 3.7 9.8 - - - +
157B LEU* 3.8 21.1 - - + +
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA 5.5 0.8 + - - -
41B PRO* 2.9 46.9 + - + +
42B VAL 3.8 4.3 - - - +
44B ARG* 1.3 75.2 - - + +
46B ILE* 1.3 60.1 + - - +
48B TYR* 4.2 4.7 - - - +
49B GLY* 2.9 26.2 + - - -
71B VAL* 3.8 14.5 - - + +
75B TYR* 3.2 43.8 + - + -
76B HIS* 3.3 25.1 + - + +
77B PRO* 4.7 6.2 - - - +
147B TYR* 6.1 1.2 - - - +
153B GLU* 2.9 40.7 + - - +
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 2.9 22.5 + - + +
43B HIS 3.1 4.7 + - - +
45B ARG* 1.3 75.0 - - - +
47B LEU* 1.3 59.4 + - - +
49B GLY 3.8 0.3 - - - -
50B MET* 2.9 38.9 + - + +
67B ILE* 5.1 0.7 - - + -
71B VAL* 4.2 10.8 - - + +
83B ILE* 3.3 46.7 - - + +
86B ALA* 3.7 12.6 - - + -
87B MET* 3.7 37.7 - - + +
90B MET* 3.5 23.1 - - + -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.0 23.1 - - + -
43B HIS 2.9 17.6 + - - +
44B ARG 3.8 3.4 - - - +
46B ILE* 1.3 77.3 - - - +
48B TYR* 1.3 56.5 - - - +
50B MET* 3.4 14.1 + - - +
51B ASN 2.9 21.8 + - - -
90B MET* 4.8 12.8 - - + -
100B LEU* 4.2 42.0 - - + +
101B VAL* 4.9 0.2 - - + -
125B MET* 4.5 5.5 - - + +
129B ALA* 4.3 11.7 - - + +
132B MET* 4.1 23.6 - - + -
133B LEU* 3.5 17.5 - - + +
157B LEU* 4.1 10.1 - - + -
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Residues in contact with TYR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG 2.9 17.9 + - - +
45B ARG* 4.2 3.4 - - - +
47B LEU* 1.3 73.5 - - - +
49B GLY* 1.3 60.2 + - - +
51B ASN* 3.0 15.4 + - - +
52B GLU* 2.9 61.4 + - + +
75B TYR* 3.6 34.8 - + - -
133B LEU* 4.8 6.6 - - + +
136B ILE* 4.8 9.2 - - + -
143B PHE* 3.4 29.7 - + - -
152B ARG 3.5 21.7 + - - -
153B GLU* 4.5 1.1 - - + -
154B PRO* 3.5 34.3 - - + -
157B LEU* 5.2 2.5 - - + -
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Residues in contact with GLY 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG 2.9 20.3 + - - -
46B ILE 3.8 0.7 - - - -
48B TYR* 1.3 76.7 - - - +
50B MET* 1.3 56.8 + - - +
52B GLU* 3.6 1.0 + - - +
53B LEU* 3.0 38.1 + - - +
67B ILE* 5.2 0.9 - - - -
70B ASP* 6.2 0.2 - - - -
71B VAL* 4.1 11.7 - - - -
75B TYR* 3.8 22.0 - - - -
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Residues in contact with MET 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 2.9 35.8 + - + +
47B LEU* 3.6 8.3 - - - +
48B TYR 3.2 0.2 - - - -
49B GLY* 1.3 73.0 - - - +
51B ASN* 1.3 66.7 + - - +
53B LEU* 3.3 2.8 + - - -
54B GLY 3.2 8.7 + - - -
55B VAL* 3.1 33.3 + - + +
67B ILE* 3.7 39.0 - - + -
87B MET* 4.3 4.3 - - + -
101B VAL* 4.1 19.3 - - + -
123B ALA* 3.9 7.4 - - + +
124B ARG* 3.5 37.9 - - - +
125B MET* 3.8 19.3 - - + -
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Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU 2.9 14.5 + - - +
48B TYR* 3.0 16.9 + - - +
50B MET* 1.3 76.3 - - - +
52B GLU* 1.3 77.8 + - - +
54B GLY* 3.0 15.2 + - - -
56B THR* 4.4 16.6 - - - +
125B MET* 4.1 8.1 - - - +
130B LEU* 5.5 2.4 - - - +
133B LEU* 3.5 23.1 - - + +
136B ILE* 3.7 28.1 - - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B TYR* 2.9 51.9 + - + +
49B GLY 4.1 2.9 - - - +
51B ASN* 1.3 89.7 + - - +
53B LEU* 1.3 62.0 + - - +
54B GLY* 3.1 1.5 + - - -
74B LYS* 4.3 9.0 - - - +
75B TYR* 3.6 23.3 - - - +
136B ILE* 5.8 0.2 - - - +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLY 3.0 26.1 + - - +
50B MET* 3.5 10.3 - - - +
51B ASN 3.1 0.2 - - - -
52B GLU* 1.3 77.3 - - - +
54B GLY* 1.3 61.1 + - - +
55B VAL* 4.3 11.2 - - + +
62B LYS* 5.6 7.6 - - + -
66B ARG* 3.4 38.6 - - + +
67B ILE* 5.1 12.1 - - + -
70B ASP* 3.4 38.1 - - + +
74B LYS* 3.9 12.8 - - - +
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B MET 3.2 0.2 + - - -
51B ASN 3.0 15.0 + - - -
52B GLU 3.1 1.9 - - - -
53B LEU* 1.3 80.7 - - - +
55B VAL* 1.3 58.8 + - - +
56B THR* 3.3 11.7 - - - -
59B LYS* 3.3 22.5 - - - +
60B PRO 5.0 0.2 - - - +
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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