Contacts of the strand formed by residues 68 - 73 (chain D) in PDB entry 1Z10
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 68 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D PRO* 3.6 30.0 - - + +
35D PRO* 3.9 11.8 - - - +
65D TYR 4.7 1.0 - - - +
66D GLY* 3.2 3.7 - - - +
67D PRO* 1.3 86.2 - - + +
69D PHE* 1.3 64.0 + - - +
79D VAL* 4.0 14.4 - - + -
80D VAL 3.4 2.7 - - - -
81D LEU* 4.0 8.3 - - + -
86D ALA* 3.8 13.9 - - + -
380D PHE* 4.0 18.8 - - + -
381D ARG* 3.7 26.2 - - - +
383D PHE* 4.1 20.4 - - + -
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Residues in contact with PHE 69 (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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34D PRO* 3.7 5.4 - - - -
35D PRO 3.1 14.6 - - - +
36D GLY* 4.7 0.4 - - - -
37D PRO* 4.9 0.4 - - + -
58D LEU* 3.3 42.4 - - + -
61D ILE* 3.4 24.7 - - + -
62D SER* 3.7 17.9 - - - -
65D TYR* 4.2 14.4 - - + -
66D GLY 3.5 15.7 - - - +
68D VAL* 1.3 76.0 - - - +
70D THR* 1.3 72.8 + - - +
71D ILE* 4.0 6.3 - - + -
79D VAL* 3.4 3.1 - - - +
80D VAL* 2.8 73.1 + - + -
82D CYS* 3.8 5.6 - - - -
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Residues in contact with THR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 3.8 10.4 - - + +
34D PRO* 2.6 45.6 + - - +
35D PRO 2.9 8.1 + - - -
36D GLY* 3.5 19.2 - - - -
37D PRO* 3.9 5.7 - - - +
45D ASN* 4.6 1.4 - - - +
69D PHE* 1.3 76.3 - - - +
71D ILE* 1.3 62.4 + - - +
72D HIS* 3.9 15.6 + - + -
77D ARG* 3.6 34.5 - - + -
78D VAL 3.4 7.9 - - - +
79D VAL* 4.2 2.7 - - + +
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Residues in contact with ILE 71 (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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37D PRO* 3.7 12.6 - - + -
45D ASN* 3.5 30.3 - - + +
49D LEU* 4.3 11.9 - - + -
58D LEU* 4.0 14.1 - - + -
61D ILE* 3.5 28.5 - - + -
69D PHE* 4.0 10.9 + - + -
70D THR* 1.3 75.6 - - - +
72D HIS* 1.3 66.2 + - - +
73D LEU* 3.7 20.2 - - + -
76D ARG 3.7 0.2 - - - +
77D ARG* 3.6 2.9 - - - -
78D VAL* 2.8 43.6 + - + +
80D VAL* 3.5 23.6 - - + -
392D TYR* 6.0 0.2 - - + -
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Residues in contact with HIS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PRO 4.9 2.0 + - - -
39D PRO* 3.6 28.7 - - + +
44D GLY* 3.6 11.2 - - - -
45D ASN* 2.7 50.3 + - - +
49D LEU* 4.2 4.3 - - - +
70D THR* 3.9 23.3 + - + -
71D ILE* 1.3 73.4 - - - +
73D LEU* 1.3 63.4 + - - +
74D GLY 3.0 17.8 + - - +
75D PRO* 5.2 3.8 - - + -
76D ARG 3.4 4.3 - - - -
77D ARG* 3.5 35.7 + - + -
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Residues in contact with LEU 73 (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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49D LEU* 3.7 24.7 - - + -
54D MET* 3.9 17.3 - - + -
58D LEU* 5.2 0.4 - - + -
71D ILE* 3.7 23.8 - - + -
72D HIS* 1.3 67.9 - - - +
74D GLY* 1.3 63.0 + - - +
75D PRO 3.3 0.5 - - - -
76D ARG* 2.8 38.7 + - + +
78D VAL* 4.0 15.3 - - + -
218D GLN* 6.2 0.4 - - - +
221D GLU* 4.8 4.3 - - + +
222D MET* 3.6 33.0 - - + +
392D TYR* 3.3 41.3 - - + +
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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