Contacts of the helix formed by residues 41 - 58 (chain A) in PDB entry 2ZLB
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 ASN 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 2.9 24.6 + - - +
34A THR* 3.1 33.0 + - + +
40A MET* 1.3 77.5 - - - +
42A VAL* 1.3 59.7 + - - +
43A GLY 3.2 0.7 + - - -
44A ASP* 3.2 22.4 + - + +
45A ALA* 3.3 17.2 + - - +
198A LEU* 3.7 17.8 - - + +
204A VAL* 4.0 4.3 - - - -
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TRP* 3.5 49.3 - - + +
39A ALA* 4.2 7.9 - - + +
40A MET 3.0 5.7 + - - +
41A ASN* 1.3 71.2 - - - +
43A GLY* 1.3 55.0 + - - +
45A ALA* 3.4 7.6 - - - +
46A LYS* 2.7 51.9 + - + +
169A ASP* 5.7 0.9 - - - +
204A VAL* 3.9 23.3 - - + +
205A ASP* 4.6 8.9 - - + +
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Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 4.3 1.1 - - - -
38A TRP* 3.4 35.4 - - - -
41A ASN* 3.1 2.9 + - - -
42A VAL* 1.3 75.6 - - - +
44A ASP* 1.3 54.8 + - - +
46A LYS* 3.7 3.3 - - - +
47A GLY 2.8 31.0 + - - -
71A TYR* 3.5 22.9 + - - -
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Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.8 10.8 + - - +
41A ASN* 3.2 22.0 + - - +
43A GLY* 1.3 70.7 - - - +
45A ALA* 1.3 62.7 + - - +
48A GLN* 3.4 38.8 + - - +
71A TYR* 4.0 2.4 + - - -
75A ARG* 5.1 4.0 - - - +
198A LEU* 3.8 18.8 - - + +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN 3.3 12.3 + - - +
42A VAL* 3.4 10.1 - - - +
44A ASP* 1.3 80.1 + - - +
46A LYS* 1.3 58.9 + - - +
48A GLN* 5.6 0.3 - - - +
49A ILE* 3.7 10.9 + - - +
196A SER* 2.9 39.2 + - - -
198A LEU* 4.1 9.4 - - + +
204A VAL* 3.8 22.4 - - + -
205A ASP* 4.1 7.2 - - + -
207A LEU* 4.2 2.1 - - - +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TRP* 5.9 1.6 - - + -
42A VAL* 2.7 35.6 + - + +
43A GLY* 3.7 5.8 - - - +
45A ALA* 1.3 73.6 - - - +
47A GLY* 1.3 68.1 + - - +
48A GLN 3.3 0.7 - - - -
49A ILE* 3.3 5.7 + - - +
50A MET* 3.0 40.5 + - - +
71A TYR* 4.6 9.6 - - + -
72A SER* 3.4 20.7 + - - -
139A PHE* 4.2 1.6 - - - -
141A ASP* 2.9 23.0 + - - -
169A ASP* 2.6 36.6 + - - +
205A ASP* 3.1 19.7 - - - +
207A LEU* 4.3 7.6 - - + -
300A SO4 4.1 6.8 + - - -
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY 2.8 20.4 + - - -
44A ASP 4.2 0.2 - - - -
46A LYS* 1.3 73.6 - - - +
48A GLN* 1.3 55.9 + - - +
50A MET* 3.1 4.8 + - - +
51A ASP* 2.8 34.5 + - - +
71A TYR* 4.6 0.7 - - - -
75A ARG* 3.3 37.9 - - - -
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Residues in contact with GLN 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 ASP* 3.4 30.2 + - - +
45A ALA 5.6 0.2 - - - +
46A LYS 3.3 0.8 - - - -
47A GLY* 1.3 75.0 - - - +
49A ILE* 1.3 63.6 + - + +
51A ASP* 3.7 9.4 - - - +
52A ALA* 3.1 22.9 + - - +
55A ARG* 6.3 0.2 - - - -
75A ARG* 2.7 25.4 + - - +
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 3.7 19.2 + - - +
46A LYS 3.3 6.3 + - - +
48A GLN* 1.3 76.0 - - + +
50A MET* 1.3 67.2 + - - +
52A ALA* 3.3 6.3 + - + +
53A VAL* 3.0 39.6 + - + +
167A LEU* 4.4 2.7 - - + -
194A TYR* 3.9 47.8 - - + -
195A SER 6.4 0.2 - - - -
196A SER* 3.9 12.1 - - - +
207A LEU* 3.9 28.7 - - + -
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Residues in contact with MET 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 3.0 40.8 + - - +
47A GLY* 3.1 11.9 + - - +
49A ILE* 1.3 75.6 - - - +
51A ASP* 1.3 57.1 + - - +
53A VAL* 3.4 1.7 + - - +
54A ILE* 2.9 39.9 + - + +
71A TYR* 5.5 0.9 - - - -
72A SER* 3.5 35.2 - - - +
75A ARG* 3.8 15.0 - - + -
76A MET* 3.6 18.6 - - + -
139A PHE* 3.7 33.7 - - + -
167A LEU* 4.1 12.6 - - + -
207A LEU* 4.5 3.8 - - + -
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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
----------------------------------------------------------
47A GLY 2.8 18.7 + - - +
48A GLN* 3.7 12.1 - - - +
50A MET* 1.3 72.0 - - - +
52A ALA* 1.3 57.1 + - - +
54A ILE* 3.4 2.1 + - - +
55A ARG* 2.9 57.4 + - - +
75A ARG* 2.7 42.7 + - - +
78A ARG* 2.8 29.6 + - - -
79A LEU* 3.5 13.6 - - + +
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Residues in contact with ALA 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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48A GLN 3.1 14.5 + - - +
49A ILE* 3.3 6.7 + - + +
51A ASP* 1.3 78.6 - - - +
53A VAL* 1.3 59.9 + - + +
55A ARG* 4.0 6.4 - - - +
56A GLU* 2.8 33.3 + - - +
194A TYR* 6.5 0.7 - - + -
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Residues in contact with VAL 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 ILE* 3.0 31.5 + - + +
50A MET 3.8 3.1 - - - +
52A ALA* 1.3 76.7 - - + +
54A ILE* 1.3 66.0 + - - +
56A GLU* 3.2 3.8 + - - +
57A TYR* 3.1 47.4 + - + +
137A MET* 4.2 15.9 - - + -
165A VAL* 4.0 20.0 - - + -
167A LEU* 4.1 24.0 - - + -
194A TYR* 4.2 17.9 - - + +
209A LYS* 4.4 6.1 - - + +
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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 MET* 2.9 35.5 + - + +
51A ASP* 3.9 4.0 - - - +
53A VAL* 1.3 74.1 - - - +
55A ARG* 1.3 59.0 + - + +
58A SER* 2.7 33.9 + - - -
59A PRO* 3.3 19.0 - - + +
62A VAL* 5.4 1.1 - - + -
75A ARG 5.5 0.2 - - - +
76A MET* 3.7 36.6 - - + +
79A LEU* 3.7 38.6 - - + +
80A LEU* 5.0 6.7 - - + -
137A MET* 3.7 30.1 - - + -
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Residues in contact with ARG 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 ASP* 2.9 43.8 + - - +
52A ALA* 4.0 6.1 - - - +
54A ILE* 1.3 77.5 - - + +
56A GLU* 1.3 64.4 + - - +
57A TYR 3.5 0.3 + - - -
58A SER* 4.0 11.0 + - - -
78A ARG* 4.5 6.5 - - - +
79A LEU* 3.8 34.1 - - + +
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Residues in contact with GLU 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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52A ALA* 2.8 23.8 + - - +
53A VAL* 3.2 6.0 + - - +
55A ARG* 1.3 75.8 - - - +
57A TYR* 1.3 95.3 + - + +
58A SER* 5.0 1.0 - - - -
194A TYR* 5.5 0.3 + - - -
209A LYS* 4.1 9.7 + - - -
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Residues in contact with TYR 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 VAL* 3.1 34.9 + - + +
56A GLU* 1.3 109.4 + - + +
58A SER* 1.3 73.9 + - - +
59A PRO* 3.2 10.6 - - + +
136A ASP* 5.8 1.1 - - - +
137A MET* 5.8 1.8 - - - -
163A GLY 5.0 3.8 - - - -
165A VAL* 3.6 31.6 - - + -
209A LYS* 2.8 38.2 + - + -
211A ILE* 3.2 24.2 - - + +
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 2.7 14.1 + - - -
55A ARG* 4.1 9.4 + - - -
56A GLU 3.6 1.7 - - - -
57A TYR* 1.3 80.0 - - - +
59A PRO* 1.3 68.5 - - - +
60A SER* 3.6 2.3 + - - -
81A GLN* 3.0 28.7 + - - +
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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
------------------------------------------------------------
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