Contacts of the strand formed by residues 2 - 9 (chain D) in PDB entry 3ZO7
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 LEU 2 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TRP* 3.5 35.9 - - + +
1D MET* 1.3 77.0 - - - +
3D TYR* 1.3 67.4 + - - +
41D ARG* 4.2 20.4 - - - +
55D VAL* 4.3 12.6 - - + -
56D PHE 3.2 3.6 - - - +
57D ASP* 3.9 32.5 - - + +
83D PRO* 3.8 2.8 - - - +
84D LEU* 3.0 48.1 + - + +
85D SER 5.9 1.8 - - - +
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Residues in contact with TYR 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 3.7 29.5 - - + +
2D LEU* 1.3 79.6 - - - +
4D LEU* 1.3 61.3 + - - +
5D VAL* 3.7 10.0 + - + +
54D SER 3.6 0.2 - - - +
55D VAL* 3.2 6.2 - - - -
56D PHE* 2.9 38.5 + - + +
58D VAL* 3.4 29.8 - - + -
60D SER* 3.5 5.2 - - - -
61D HIS* 2.7 49.4 + + - -
64D LEU* 3.5 32.1 - - + -
81D VAL* 3.8 13.5 - - + -
82D GLU 3.5 4.9 - - - +
83D PRO* 4.3 16.8 - - + -
84D LEU* 4.0 4.0 - - - -
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Residues in contact with LEU 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.8 13.0 - - + -
6A ARG* 4.2 10.1 - - - +
44A TRP* 5.4 1.1 - - + -
53A ILE* 4.3 27.1 - - + -
3D TYR* 1.3 71.2 - - - +
5D VAL* 1.3 63.0 + - - +
6D ARG* 5.3 3.1 - - + +
44D TRP* 5.6 0.4 - - + -
53D ILE* 3.7 25.6 - - + -
54D SER 3.5 14.6 - - - +
55D VAL* 4.3 11.9 - - + -
80D ASP* 3.5 3.5 - - - +
81D VAL* 3.6 1.2 - - - -
82D GLU* 2.8 65.3 + - + +
84D LEU* 3.8 16.9 - - + +
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Residues in contact with VAL 5 (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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3D TYR* 4.1 15.9 - - + +
4D LEU* 1.3 80.8 - - - +
6D ARG* 1.3 61.9 + - - +
7D MET* 3.9 25.7 + - + -
52D ASN* 3.9 1.6 - - - +
53D ILE* 3.7 1.9 - - - -
54D SER* 2.8 40.3 + - - +
56D PHE* 3.7 29.6 - - + -
64D LEU* 4.7 6.7 - - + -
68D LEU* 4.4 5.4 - - + -
79D ILE* 3.9 20.9 - - + -
80D ASP 3.3 7.6 - - - +
81D VAL* 4.2 13.9 - - + -
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Residues in contact with ARG 6 (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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4A LEU* 4.2 6.5 - - - +
6A ARG* 5.7 4.8 - - - +
82A GLU* 2.7 43.2 + - - -
4D LEU* 4.2 4.2 - - + +
5D VAL* 1.3 73.6 - - - +
7D MET* 1.3 68.9 + - - +
8D THR* 4.9 9.4 - - - +
46D THR* 4.0 11.1 - - + +
52D ASN 3.6 5.8 - - - +
53D ILE* 3.3 29.9 - - + +
78D THR 3.5 1.6 - - - +
79D ILE* 3.3 5.7 - - - +
80D ASP* 3.0 48.6 + - + +
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Residues in contact with MET 7 (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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5D VAL* 3.9 15.9 - - + -
6D ARG* 1.3 80.5 - - - +
8D THR* 1.3 64.6 + - - +
9D VAL* 5.7 0.9 - - + -
40D TRP* 3.8 20.9 - - + -
46D THR* 5.3 1.2 - - - +
51D GLY* 3.1 5.1 - - - -
52D ASN* 3.0 60.0 + - - +
54D SER* 4.2 0.2 - - - +
56D PHE* 3.7 33.4 - - + -
68D LEU* 3.9 11.4 - - + -
71D LEU* 4.1 7.0 - - + -
77D LEU* 4.0 31.2 - - + -
78D THR 3.4 4.5 - - - +
79D ILE* 4.4 7.6 - - + -
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Residues in contact with THR 8 (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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6D ARG* 4.9 10.4 - - - +
7D MET* 1.3 77.5 + - - +
9D VAL* 1.3 71.9 + - - +
10D ASN* 3.8 3.8 + - + +
49D LYS* 6.5 1.3 - - + -
50D TYR 4.0 6.7 - - - +
51D GLY* 4.3 0.6 - - - -
76D TYR 3.5 1.6 - - - +
77D LEU* 3.3 6.1 - - - -
78D THR* 2.9 49.1 + - - +
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Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D MET* 5.5 1.3 - - + -
8D THR* 1.3 77.1 - - - +
10D ASN* 1.3 63.0 + - - +
11D LEU* 3.7 33.7 + - + -
50D TYR* 2.9 65.8 + - + +
51D GLY* 4.7 4.9 - - - -
52D ASN* 6.0 2.2 - - - +
73D PHE* 4.6 15.7 - - + -
76D TYR* 3.7 5.2 - - + +
77D LEU* 3.4 20.9 - - + -
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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
------------------------------------------------------------
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