Contacts of the strand formed by residues 27 - 35 (chain B) in PDB entry 1ZQ1
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 GLU 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLU* 3.2 8.3 - - - +
24B GLU* 3.0 32.4 + - + +
25B ASP* 2.6 14.8 + - + +
26B GLY* 1.3 78.9 - - - +
28B GLU* 1.3 64.1 + - - +
29B VAL* 5.0 0.2 - - + -
114D LYS* 3.7 37.4 + - + +
452D LYS* 5.0 11.9 - - - +
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Residues in contact with GLU 28 (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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21B THR* 5.0 15.1 - - + +
22B LYS 4.0 4.3 - - - +
23B GLU* 4.8 6.3 - - + +
26B GLY 5.3 0.4 - - - +
27B GLU* 1.3 78.8 + - - +
29B VAL* 1.3 75.2 + - - +
30B THR* 5.8 2.0 - - + -
66B ARG* 5.5 4.9 + - - -
114D LYS* 4.3 11.8 + - - -
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Residues in contact with VAL 29 (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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21B THR* 3.2 7.1 - - - -
22B LYS* 3.0 50.1 + - - +
24B GLU* 4.0 13.2 - - + -
27B GLU 5.0 0.4 - - - -
28B GLU* 1.3 83.8 - - - +
30B THR* 1.3 65.3 + - - +
31B TYR* 3.8 30.7 - - + +
114D LYS* 3.7 32.5 - - + +
143D THR* 4.0 4.5 - - - +
144D ASP* 4.0 18.8 - - + +
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Residues in contact with THR 30 (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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19B ARG* 4.0 12.0 - - - +
20B ILE 3.4 5.7 + - - -
21B THR* 3.4 22.0 - - - +
28B GLU* 5.8 2.9 - - + -
29B VAL* 1.3 80.3 - - - +
31B TYR* 1.3 71.1 + - - +
32B GLU* 5.2 2.2 - - - +
144D ASP* 4.1 17.6 + - - +
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Residues in contact with TYR 31 (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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19B ARG* 3.3 2.4 - - - +
20B ILE* 2.9 39.7 + - + +
22B LYS* 3.1 35.3 + - + -
29B VAL* 3.8 13.8 - - + +
30B THR* 1.3 78.3 - - - +
32B GLU* 1.3 71.5 + - - +
33B GLY 4.3 0.2 - - - -
49B LEU* 3.6 18.6 - - + -
51B LEU* 4.6 6.7 - - + -
57B ILE* 3.6 33.9 - - + -
59B ILE* 3.2 33.5 - - + +
114D LYS 4.7 1.0 + - - -
115D PRO 4.2 9.0 + - - -
116D VAL* 4.4 9.4 - - - +
143D THR* 3.4 28.2 + - + -
144D ASP* 5.6 0.4 - - - -
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Residues in contact with GLU 32 (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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17B PHE* 4.1 17.8 - - + -
18B VAL 3.3 8.3 - - - +
19B ARG* 2.6 49.2 + - + -
30B THR* 5.2 2.7 - - + +
31B TYR* 1.3 83.5 - - - +
33B GLY* 1.3 57.3 + - - +
49B LEU* 4.0 2.0 - - - -
51B LEU* 3.8 17.5 - - - +
52B GLU* 3.9 10.7 + - + +
70B LEU* 3.6 8.5 - - - +
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Residues in contact with GLY 33 (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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17B PHE* 3.6 14.5 - - - -
18B VAL 2.8 28.5 + - - -
32B GLU* 1.3 74.5 - - - +
34B TYR* 1.3 58.6 + - - -
49B LEU* 3.0 27.7 - - - +
50B LYS 3.0 15.7 - - - -
51B LEU* 4.0 0.7 - - - -
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Residues in contact with TYR 34 (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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15B GLY* 3.9 18.2 - - - +
16B ASP 3.5 6.3 - - - +
17B PHE* 3.4 46.6 - + + -
33B GLY* 1.3 73.2 - - - -
35B ILE* 1.3 66.2 + - - +
36B MSE 3.4 8.0 + - - +
49B LEU* 3.5 1.3 - - - -
50B LYS* 2.8 51.3 + - + +
51B LEU 5.3 0.4 - - - -
52B GLU* 4.5 17.6 + - + +
71B GLU* 5.3 0.9 + - - -
72B ARG 5.8 1.1 - - - -
74B LYS* 3.6 37.9 + - + -
110B GLU 6.0 1.8 - - - -
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Residues in contact with ILE 35 (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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7B LEU* 3.9 23.8 - - + -
12B ILE* 3.0 32.5 - - + -
13B ASN 4.2 2.5 - - - +
14B VAL* 3.7 11.5 - - + +
15B GLY* 3.0 30.1 + - - +
16B ASP 3.0 19.1 + - - +
18B VAL* 3.5 19.7 - - + -
34B TYR* 1.3 72.7 - - - +
36B MSE 1.3 72.0 + - - +
47B LEU* 3.8 30.1 - - + -
48B VAL 3.9 4.0 - - - -
49B LEU* 4.2 7.2 - - + -
67B ILE* 5.4 1.8 - - + -
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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