Contacts of the strand formed by residues 70 - 75 (chain A) in PDB entry 1CZV
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 ALA 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ILE* 3.8 6.8 - - - +
69A THR* 1.3 83.4 + - - +
71A ILE* 1.3 63.0 + - - +
124A LYS* 4.1 16.2 - - - -
125A ASN 3.3 14.6 - - - +
126A PHE* 3.9 17.7 - - + -
127A PHE* 3.6 8.5 - - - -
153A LEU* 3.7 2.6 - - - -
154A PHE* 3.0 38.5 + - + +
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Residues in contact with ILE 71 (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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70A ALA* 1.3 77.1 - - - +
72A ILE* 1.3 74.1 + - - +
73A THR* 4.1 17.3 - - + -
88A TYR* 3.6 21.0 + - + +
90A ILE* 4.3 12.6 - - + -
123A VAL 3.7 0.9 - - - +
124A LYS* 3.3 3.6 - - - +
125A ASN* 3.0 36.4 + - + +
127A PHE* 3.7 21.1 - - + -
138A VAL* 4.2 24.2 - - + -
151A LEU* 4.3 6.1 - - + -
152A GLU 3.4 13.9 - - - +
153A LEU* 3.8 17.5 - - + -
154A PHE* 4.5 1.1 - - - -
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Residues in contact with ILE 72 (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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38A LEU* 3.8 27.8 - - + -
71A ILE* 1.3 79.9 - - - +
73A THR* 1.3 66.8 + - - +
122A HIS* 3.9 33.0 - - + -
123A VAL 3.3 5.6 - - - +
124A LYS* 3.6 30.7 - - + +
151A LEU* 3.0 28.8 - - - +
152A GLU* 3.0 15.2 + - + +
154A PHE* 3.6 28.5 - - + -
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Residues in contact with THR 73 (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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71A ILE* 4.1 13.7 - - + -
72A ILE* 1.3 80.3 - - - +
74A GLN* 1.3 62.2 + - - +
85A VAL* 4.9 1.2 + - - -
88A TYR* 3.7 40.2 + - + +
115A GLY* 4.3 6.1 - - - -
116A ASN* 2.8 40.1 + - - -
121A GLY 3.9 0.9 - - - +
123A VAL* 3.2 20.6 + - - +
138A VAL* 5.2 1.8 - - + -
149A LEU* 3.7 23.1 - - + -
150A ARG 3.4 3.8 - - - -
151A LEU* 4.7 4.0 - - + -
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Residues in contact with GLN 74 (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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38A LEU* 3.4 11.0 - - + +
39A ASN* 2.7 47.5 + - - -
73A THR* 1.3 75.9 - - - +
75A GLY* 1.3 63.2 + - - +
116A ASN* 3.7 10.5 - - - +
119A THR 4.1 0.7 - - - +
120A LYS* 3.0 39.3 + - - +
121A GLY 3.9 2.5 - - - +
122A HIS* 3.0 16.5 - - - +
148A THR 4.0 0.3 - - - +
149A LEU* 3.7 9.7 - - - +
150A ARG* 2.7 57.6 + - + +
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Residues in contact with GLY 75 (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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74A GLN* 1.3 77.2 - - - +
76A CYS* 1.3 57.8 + - - +
83A MET 3.5 10.5 - - - -
84A TYR* 3.8 17.0 - - - -
116A ASN* 4.1 5.7 + - - +
119A THR 3.1 15.5 + - - -
121A GLY 4.7 0.2 + - - -
148A THR* 4.4 4.9 - - - -
150A ARG* 2.6 39.0 + - - +
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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