Contacts of the helix formed by residues 43 - 58 (chain A) in PDB entry 3ZLY
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 ASP 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLU 4.3 0.4 + - - -
42A LEU* 1.3 76.5 - - - +
44A GLU* 1.3 58.2 + - - +
45A GLN* 3.1 15.3 + - - +
46A GLN* 3.0 50.0 + - - +
47A ARG* 3.0 28.2 + - - +
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Residues in contact with GLU 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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43A ASP* 1.3 72.6 - - - +
45A GLN* 1.4 62.7 + - - +
47A ARG* 3.3 11.4 + - + +
48A LYS* 3.1 29.3 + - + +
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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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43A ASP* 3.1 10.5 + - - +
44A GLU* 1.4 76.6 - - - +
46A GLN* 1.3 64.8 + - - +
48A LYS* 3.6 15.7 + - + +
49A ARG* 3.0 73.0 + - + +
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Residues in contact with GLN 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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41A GLU 4.7 1.7 - - - +
42A LEU* 3.7 20.1 - - + +
43A ASP* 3.0 45.3 + - - +
45A GLN* 1.3 78.3 - - + +
47A ARG* 1.4 64.0 + - - +
49A ARG* 3.3 11.1 + - - +
50A LEU* 3.1 24.6 + - - +
124A PRO* 3.5 30.8 - - + +
125A TYR* 3.0 30.5 + - - -
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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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42A LEU* 4.3 19.0 - - + +
43A ASP 3.0 18.5 + - - +
44A GLU* 3.6 10.5 - - - +
46A GLN* 1.4 75.2 - - - +
48A LYS* 1.3 56.8 + - - +
50A LEU* 3.5 5.3 + - - +
51A GLU* 3.1 30.4 + - + +
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Residues in contact with LYS 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 GLU* 3.1 20.2 + - + +
45A GLN* 3.7 15.7 - - + +
46A GLN 3.3 0.2 - - - -
47A ARG* 1.3 74.7 - - - +
49A ARG* 1.4 63.1 + - + +
51A GLU* 3.4 13.1 + - - +
52A ALA* 2.9 29.2 + - + +
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Residues in contact with ARG 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* 3.0 60.6 + - + +
46A GLN* 3.3 9.9 + - - +
48A LYS* 1.4 75.6 - - + +
50A LEU* 1.3 60.3 + - - +
52A ALA* 3.4 6.8 + - - +
53A PHE* 2.9 30.1 + - - +
201A ARG* 3.3 69.9 + - - +
203A GLU* 3.5 28.9 + - - +
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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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42A LEU* 3.6 26.9 - - + -
46A GLN 3.1 15.2 + - - +
47A ARG 3.5 6.1 - - - +
49A ARG* 1.3 78.4 - - - +
51A GLU* 1.3 60.2 + - - +
53A PHE* 3.5 10.6 + - + +
54A LEU* 3.2 35.8 + - + +
122A ASN* 3.9 30.1 - - + +
123A SER* 3.8 32.1 - - - +
124A PRO* 4.2 5.4 - - + -
205A LYS* 6.4 0.2 - - - +
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Residues in contact with GLU 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* 3.1 18.7 + - + +
48A LYS* 3.7 14.1 - - - +
49A ARG 3.3 0.2 - - - -
50A LEU* 1.3 74.5 - - - +
52A ALA* 1.4 59.7 + - - +
54A LEU* 3.4 10.3 + - - +
55A THR* 2.8 39.4 + - - +
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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 LYS* 2.9 20.2 + - + +
49A ARG* 3.4 8.0 + - - +
51A GLU* 1.4 74.0 - - - +
53A PHE* 1.4 63.3 + - - +
55A THR* 3.5 6.8 + - - -
56A GLN* 3.0 31.2 + - + +
201A ARG* 6.1 1.8 - - - +
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Residues in contact with PHE 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 ARG 2.9 17.6 + - - +
50A LEU* 3.6 13.5 - - + +
52A ALA* 1.4 75.7 - - - +
54A LEU* 1.3 67.1 + - + +
56A GLN* 3.2 13.4 + - - +
57A LYS* 2.9 40.3 + - + +
122A ASN* 5.6 6.3 - - - -
128A GLY* 3.6 31.0 - - - -
129A PHE 3.7 20.9 - - - -
130A TYR* 3.4 42.2 - + - -
144A GLU* 4.1 18.4 - - + -
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Residues in contact with LEU 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 LEU* 3.2 28.1 + - + +
51A GLU* 3.4 8.0 + - - +
53A PHE* 1.3 77.4 - - + +
55A THR* 1.3 61.0 + - - +
57A LYS* 3.3 19.7 + - + +
58A GLN* 2.9 50.4 + - + +
119A HIS 5.6 1.1 - - - +
122A ASN* 3.9 34.1 - - + +
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLU* 2.8 30.9 + - - +
52A ALA* 3.7 7.8 - - - -
54A LEU* 1.3 76.8 - - - +
56A GLN* 1.4 61.2 + - - +
58A GLN* 3.7 14.8 + - - +
59A LYS* 3.5 33.3 + - - +
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Residues in contact with GLN 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* 3.0 18.7 + - - +
53A PHE* 3.2 14.1 + - - +
55A THR* 1.4 73.8 - - - +
57A LYS* 1.3 63.5 + - - +
59A LYS* 3.3 27.5 + - + +
60A VAL* 3.6 10.5 - - - +
92A LEU* 3.8 35.0 - - + +
130A TYR* 4.6 9.7 + - - +
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Residues in contact with LYS 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 PHE* 2.9 28.6 + - + +
54A LEU* 3.5 17.4 - - + +
56A GLN* 1.3 76.1 - - - +
58A GLN* 1.3 56.3 + - + +
59A LYS 3.1 0.2 - - - -
60A VAL* 3.0 31.7 + - + +
61A GLY 4.2 2.3 + - - -
118A LEU 5.1 0.2 + - - -
119A HIS* 2.8 55.9 + - - +
122A ASN* 5.4 4.4 - - - +
129A PHE* 2.9 25.4 + - - +
130A TYR* 4.0 27.7 - - + +
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Residues in contact with GLN 58 (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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54A LEU* 2.9 42.2 + - - +
55A THR* 4.0 11.9 - - - +
56A GLN 3.4 0.4 - - - -
57A LYS* 1.3 71.6 - - + +
59A LYS* 1.3 59.2 + - + +
60A VAL 3.4 0.4 + - - -
61A GLY* 4.6 4.5 + - - -
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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
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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