Contacts of the strand formed by residues 68 - 73 (chain F) in PDB entry 3ZXR
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 ASP 68 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A ARG* 3.0 52.1 + - + +
347A ARG* 3.2 2.4 + - - +
352A ARG* 3.0 41.9 + - - -
354A PRO* 3.5 2.1 - - - +
355A ILE* 3.1 37.4 + - + +
52F ALA* 5.8 4.0 - - + -
53F PHE 3.7 7.6 - - - +
67F SER* 1.3 79.9 + - - +
69F MET* 1.3 60.9 + - - +
98F PRO* 3.4 5.6 - - + +
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Residues in contact with MET 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A ARG* 3.3 29.8 - - - -
52F ALA* 3.4 8.1 - - - +
53F PHE* 3.1 53.6 + - + -
55F GLY* 4.0 6.7 - - - -
61F PHE* 5.2 2.2 - - + -
62F GLN* 3.6 21.1 - - + -
67F SER 3.5 11.4 - - - +
68F ASP* 1.3 73.9 - - - +
70F LEU* 1.3 61.9 + - - +
95F VAL* 3.8 6.7 - - + -
96F HIS 3.5 21.5 - - - +
97F ASP* 4.2 4.5 - - + +
98F PRO* 3.9 8.9 - - - +
104F TYR* 3.5 40.6 - - + -
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Residues in contact with LEU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ASP 3.4 26.0 - - - +
50F GLY 4.1 1.1 - - - -
51F LEU* 3.5 20.0 - - - +
52F ALA* 4.7 3.4 - - + +
69F MET* 1.3 76.9 - - - +
71F LEU* 1.3 66.3 + - - +
72F LEU* 4.6 11.7 - - + -
95F VAL* 3.3 8.3 - - - +
96F HIS* 2.7 56.4 + - + +
97F ASP 4.4 1.3 - - - +
98F PRO* 4.2 14.6 - - + +
101F LEU* 3.6 31.6 - - + -
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Residues in contact with LEU 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F VAL* 4.0 8.7 - - + -
25F PHE* 3.5 41.1 - - + -
35F PHE* 3.7 25.6 - - + -
50F GLY* 3.1 9.7 - - - -
51F LEU* 2.8 38.5 + - + +
53F PHE* 3.4 39.3 - - + -
70F LEU* 1.3 72.5 - - - +
72F LEU* 1.3 61.8 + - - +
93F PHE* 3.6 20.7 - - + -
94F PHE 3.2 8.3 - - - +
95F VAL* 3.8 15.3 - - + -
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F VAL 4.5 0.4 - - - +
47F PHE 3.9 18.2 - - - +
48F ASP 4.5 3.8 - - - +
49F ASP 4.1 6.1 - - - +
50F GLY* 3.7 28.7 - - - +
70F LEU* 4.6 9.9 - - + -
71F LEU* 1.3 74.1 - - - +
73F PRO* 1.4 69.7 - - + +
93F PHE* 3.3 3.8 - - - -
94F PHE* 2.8 40.2 + - + +
96F HIS* 3.6 43.5 - - + +
101F LEU* 5.1 6.7 - - + +
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Residues in contact with PRO 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F VAL* 3.4 23.3 - - + +
47F PHE* 3.5 52.0 - - + +
72F LEU* 1.4 91.4 - - + +
74F ASP* 1.3 58.9 + - - +
75F PRO* 3.5 7.9 - - - +
91F ILE* 4.3 8.5 - - + -
92F ASN 3.9 0.2 - - - +
93F PHE* 3.3 33.8 - - + -
94F PHE* 4.7 4.0 - - - -
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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