Contacts of the strand formed by residues 77 - 84 (chain D) in PDB entry 2ZOT
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 SER 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C ARG* 3.0 51.7 + - - +
56C GLU 3.4 24.2 + - - -
57C GLY 4.8 0.2 - - - -
58C TYR 3.0 18.9 + - - +
59C THR* 5.0 1.2 - - - -
75D GLY 4.0 1.2 + - - -
76D THR* 1.3 77.6 - - - +
78D TYR* 1.3 58.6 + - - +
146D PHE* 3.4 17.7 - - - +
147D TRP 4.0 6.1 - - - -
148D ILE* 4.4 1.6 - - - +
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Residues in contact with TYR 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D VAL* 3.7 28.9 - - + -
66D GLU 4.9 4.5 - - - -
69D PRO* 3.6 24.4 - - + +
71D PHE 4.6 0.2 + - - -
72D TYR* 3.2 16.6 - - + -
73D LYS* 2.9 32.4 + - - +
76D THR* 3.3 43.7 - - + +
77D SER* 1.3 73.3 - - - +
79D ARG* 1.3 62.4 + - - +
80D VAL* 3.4 4.0 + - + +
146D PHE* 3.2 5.9 - - - -
147D TRP* 2.7 62.8 + + + +
149D ALA* 4.0 13.2 - - + -
181D LEU* 5.8 1.1 - - + -
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Residues in contact with ARG 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ARG* 3.0 34.2 - - - +
60C GLU* 5.8 0.2 + - - -
168C ILE* 6.1 2.6 - - - +
170C TYR* 3.0 29.1 + - - -
64D ARG 4.0 0.3 - - - +
65D VAL* 3.6 4.6 - - - +
66D GLU* 3.2 54.6 + - + +
77D SER 4.0 2.2 + - - -
78D TYR* 1.3 70.7 - - - +
80D VAL* 1.3 60.5 + - - +
81D THR* 4.5 4.3 - - - +
117D ILE* 3.7 12.1 - - - +
142D ARG* 6.2 1.8 - - - +
144D GLN* 2.8 48.0 + - + +
145D VAL 3.7 7.0 - - - +
146D PHE* 3.8 10.8 - - + -
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D LEU* 3.8 25.6 - - + -
64D ARG 3.8 5.2 - - - +
65D VAL* 4.3 19.1 - - + -
78D TYR* 3.7 14.6 - - + +
79D ARG* 1.3 76.7 - - - +
81D THR* 1.3 64.8 + - - +
95D LEU* 4.4 13.2 - - + +
114D PHE* 5.0 3.6 - - + -
143D ILE* 5.4 1.3 - - - +
144D GLN* 3.1 5.5 - - - +
145D VAL* 2.8 51.4 + - + +
147D TRP* 3.8 21.1 - - + -
159D LEU* 4.3 12.1 - - + -
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Residues in contact with THR 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D SER 3.6 1.0 - - - +
63D LEU* 3.3 8.8 - - - +
64D ARG* 3.0 37.8 + - + +
66D GLU* 3.3 24.8 + - - +
79D ARG* 4.5 2.9 - - - +
80D VAL* 1.3 77.5 + - - +
82D LEU* 1.3 62.6 + - - +
83D SER* 3.3 21.3 - - - +
142D ARG* 3.8 29.4 + - + +
143D ILE 3.4 7.4 - - - +
144D GLN* 3.5 18.2 + - - +
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D PHE* 4.6 2.5 - - + -
62D SER 3.3 15.0 - - - +
63D LEU* 4.3 7.9 - - + +
81D THR* 1.3 73.8 - - - +
83D SER* 1.3 64.2 + - - +
90D PHE* 3.8 16.0 - - + -
93D PHE* 3.7 41.1 - - + -
95D LEU* 5.6 1.6 - - + -
142D ARG* 3.2 6.8 - - - +
143D ILE* 3.0 42.4 + - + +
161D ALA* 4.2 18.6 - - + -
163D ILE* 4.4 14.6 - - + -
177D LEU* 3.8 24.2 - - + -
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Residues in contact with SER 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLU 3.6 1.0 - - - +
61D PHE* 3.2 9.0 - - - +
62D SER* 2.8 45.4 + - - -
64D ARG* 4.7 8.6 - - - -
81D THR* 3.3 22.7 + - - +
82D LEU* 1.3 72.9 - - - +
84D ALA* 1.3 59.7 + - - +
85D ALA* 3.6 14.3 + - - -
90D PHE* 4.4 3.6 - - - -
141D THR 3.5 5.2 - - - -
142D ARG* 4.6 6.3 + - - +
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLU 3.6 7.0 - - - -
61D PHE* 3.7 17.5 - - + -
83D SER* 1.3 72.2 - - - +
85D ALA* 1.3 55.6 + - - +
86D PRO* 2.9 24.9 - - - +
88D SER* 3.4 31.0 - - - +
90D PHE* 3.9 10.1 - - + -
141D THR* 2.7 27.7 + - - +
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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
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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