Contacts of the strand formed by residues 40 - 46 (chain A) 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 TRP 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A MET* 3.9 22.9 - - + -
31A SER* 3.4 33.9 - - - -
34A LEU* 3.1 38.4 + - + -
35A GLN* 3.3 30.4 - - + +
38A GLY 4.4 1.3 - - - -
39A GLN* 1.3 75.8 - - - +
41A ARG* 1.3 64.5 + - - +
42A TYR 3.2 22.7 + - - -
43A LEU* 3.7 26.8 - - + +
52A ASN* 4.5 4.0 - - - -
54A SER* 3.0 31.0 + - - -
55A VAL 4.2 1.3 - - - -
56A PHE* 3.5 23.1 - + + -
71A LEU* 3.9 24.5 - - + -
90D ARG* 4.3 0.2 + - - -
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 4.0 34.7 - - - +
35A GLN 5.8 0.2 - - - -
38A GLY* 4.4 14.8 - - - +
39A GLN 3.5 1.6 - - - -
40A TRP* 1.3 74.0 - - - +
42A TYR* 1.3 105.3 + - + +
55A VAL* 2.8 20.6 + - + +
57A ASP* 4.0 23.8 + - + -
44D TRP* 4.5 7.7 - - - +
90D ARG* 3.0 20.3 + - - -
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Residues in contact with TYR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TRP* 3.2 14.5 + - - -
41A ARG* 1.3 120.1 + - + +
43A LEU* 1.3 61.0 + - - +
44A TRP* 3.6 35.4 - + + -
53A ILE 4.6 0.4 - - - -
54A SER* 3.3 1.2 - - - -
55A VAL* 3.1 46.5 + - + -
42D TYR* 3.3 40.3 + + - -
44D TRP* 3.9 20.6 - + - -
90D ARG* 3.8 16.2 - - - +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A SER* 5.0 2.9 - - - +
35A GLN* 4.0 17.7 - - - +
40A TRP* 3.7 22.7 - - + +
42A TYR* 1.3 77.4 - - - +
44A TRP* 1.3 69.7 + - - +
52A ASN* 3.5 29.8 - - + +
53A ILE 3.7 2.2 - - - -
54A SER* 3.4 18.2 - - - +
87D HIS* 3.7 39.4 + - + +
89D ALA* 4.1 6.1 - - + -
90D ARG* 3.8 42.0 - - - +
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Residues in contact with TRP 44 (chain A).
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* 5.6 0.4 - - + -
42A TYR* 3.6 40.8 - + + -
43A LEU* 1.3 81.8 + - - +
45A ARG* 1.3 60.2 + - - +
52A ASN* 3.1 6.9 - - - +
53A ILE* 2.9 60.0 + - + +
55A VAL* 4.3 12.6 - - + -
2D LEU* 3.5 30.6 - - + +
4D LEU* 5.4 1.6 - - + -
41D ARG* 6.2 1.5 - - - +
42D TYR* 4.0 21.5 - + - -
44D TRP* 4.6 2.9 - + - -
55D VAL* 3.8 29.4 - - + -
84D LEU* 3.9 35.2 - - + -
85D SER 3.7 12.1 - - - +
86D HIS* 5.7 2.2 - - - -
87D HIS* 3.8 5.6 - - - -
90D ARG* 6.0 1.8 - - - +
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Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TRP* 1.3 72.9 - - - +
46A THR* 1.3 67.2 + - - +
47A THR* 3.2 4.7 + - - +
48A GLY 5.5 0.7 - - - +
49A LYS 3.5 17.4 + - - -
50A TYR* 4.5 14.9 - - - -
51A GLY* 3.0 33.9 + - - +
84D LEU* 3.7 6.2 - - - +
85D SER* 2.8 54.5 + - - +
86D HIS 3.9 10.5 - - - +
87D HIS* 3.2 33.7 + - + +
88D PRO* 3.7 28.9 - - - +
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG* 4.2 16.2 - - + +
7A MET 4.8 2.1 + - - +
44A TRP 3.6 0.4 + - - -
45A ARG* 1.3 72.2 - - - +
47A THR* 1.3 68.0 + - - +
49A LYS* 2.9 42.0 + - + +
51A GLY* 3.4 20.3 + - - -
52A ASN 3.6 25.8 - - - +
53A ILE* 3.7 19.1 - - + -
82D GLU* 4.4 6.7 - - - +
83D PRO 4.7 3.4 - - - -
84D LEU* 5.2 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