Contacts of the strand formed by residues 19 - 25 (chain B) in PDB entry 2Z9I
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 VAL 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B VAL* 3.8 16.6 - - + +
16B VAL 3.2 13.1 + - - +
17B PRO 4.2 2.9 - - - +
18B SER* 1.3 82.6 - - - +
20B VAL* 1.3 75.2 + - - +
35B GLY 3.3 12.6 - - - +
36B ILE* 4.9 0.9 - - + -
69B THR 4.8 0.2 - - - +
71B SER* 4.5 10.7 + - - -
103B ILE* 4.7 2.0 - - + -
120B ILE* 3.5 44.4 - - + +
121B GLY* 4.3 7.0 - - - -
122B SER* 5.9 0.2 - - - +
128B GLY* 6.3 1.6 - - - -
171B GLY* 4.6 2.2 - - - -
172B ALA* 3.8 28.9 - - + +
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Residues in contact with VAL 20 (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 PRO 5.1 0.2 - - - +
19B VAL* 1.3 81.9 - - - +
21B MSE 1.3 57.7 + - - +
22B LEU* 3.8 16.2 - - + -
34B SER* 3.2 8.5 - - - -
35B GLY* 2.8 45.3 + - - +
37B ILE* 3.7 20.9 - - + -
44B ILE* 3.9 7.9 - - + -
68B VAL* 3.6 20.4 - - + -
69B THR 3.5 11.7 - - - +
70B PHE* 3.6 31.6 - - + -
122B SER* 4.2 3.2 + - - -
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Residues in contact with MSE 21 (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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20B VAL* 1.3 74.0 - - - +
22B LEU* 1.3 69.9 + - - +
23B GLU* 3.2 29.8 - - + +
32B GLU* 2.9 44.2 - - + +
33B GLY 3.3 12.6 - - - +
67B THR 3.5 1.0 - - - +
68B VAL* 3.3 7.3 - - - +
69B THR* 3.0 45.4 + - - +
122B SER* 3.3 17.5 + - - +
125B GLY* 3.8 27.4 - - - +
127B GLU* 4.5 13.0 - - + +
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Residues in contact with LEU 22 (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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20B VAL* 3.8 14.1 - - + -
21B MSE 1.3 81.8 - - - +
23B GLU* 1.3 64.0 + - - +
31B GLU 3.9 0.6 - - - +
32B GLU* 3.4 3.8 - - - +
33B GLY 2.8 36.5 + - - +
34B SER 3.6 11.4 - - - +
35B GLY* 4.2 2.5 - - - +
44B ILE* 4.5 1.8 - - + -
46B THR* 3.4 41.7 - - + +
50B VAL* 4.0 14.0 - - + +
51B ILE* 3.9 13.2 - - + -
67B THR 3.4 2.0 - - - -
68B VAL* 3.7 25.6 - - + -
78B PHE* 4.1 12.8 - - + -
92B VAL* 4.2 13.2 - - + -
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Residues in contact with GLU 23 (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 MSE 3.2 33.4 - - + +
22B LEU* 1.3 79.4 - - - +
24B THR* 1.3 65.3 + - - +
25B ASP 4.2 0.7 - - - +
31B GLU 3.5 4.7 - - - +
32B GLU* 3.7 11.0 - - + +
65B LYS 3.7 0.4 - - - +
66B THR* 3.2 4.7 - - - -
67B THR* 2.7 53.3 + - - +
69B THR* 4.1 14.7 + - - -
78B PHE* 3.8 2.8 - - - -
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Residues in contact with THR 24 (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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23B GLU* 1.3 76.3 + - - +
25B ASP* 1.3 63.6 + - - +
30B SER* 3.1 5.9 + - - -
31B GLU* 3.0 42.8 + - - +
50B VAL 4.1 11.8 + - - -
51B ILE* 4.9 1.9 - - - +
53B ALA* 3.4 36.6 + - + +
64B PRO 4.6 10.1 - - - -
65B LYS 3.2 8.7 - - - +
66B THR* 4.4 7.4 - - + -
78B PHE* 3.7 17.2 - - - -
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Residues in contact with ASP 25 (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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23B GLU* 4.2 0.8 - - - +
24B THR* 1.3 78.3 - - - +
30B SER* 4.2 22.4 - - - +
64B PRO* 4.4 9.9 - - - +
65B LYS* 2.8 43.6 + - + +
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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