Contacts of the strand formed by residues 69 - 75 (chain A) in PDB entry 5ZF6
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 GLY 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ALA* 3.1 5.3 - - - +
68A ASP* 1.3 80.2 - - - +
70A SER* 1.3 61.2 + - - -
83A THR* 3.5 2.3 - - - -
84A ALA* 2.8 31.5 + - - +
176A ALA* 3.8 11.3 - - - +
179A LEU* 4.7 3.6 - - - -
180A SER* 3.7 16.6 - - - -
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Residues in contact with SER 70 (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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60A SER* 3.8 7.3 + - - -
61A GLY* 3.1 32.4 + - - -
67A ALA* 4.9 4.6 - - - +
69A GLY* 1.3 76.6 - - - -
71A ALA* 1.3 66.2 + - - +
81A MET* 3.9 10.0 - - - +
82A VAL 3.3 5.8 - - - -
83A THR* 3.7 21.1 - - - -
176A ALA* 4.1 4.0 + - - -
179A LEU* 3.6 19.8 - - - +
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Residues in contact with ALA 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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59A SER 3.4 7.0 - - - +
60A SER* 4.2 3.1 - - - +
61A GLY* 4.4 0.4 - - - +
70A SER* 1.3 79.3 - - - +
72A VAL* 1.3 66.3 + - - +
80A VAL 3.8 0.2 - - - +
81A MET* 3.2 5.6 - - - +
82A VAL* 2.9 30.2 + - - -
172A GLY* 3.9 11.9 - - - +
175A VAL* 3.6 33.0 - - + -
176A ALA* 3.6 14.1 - - + +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU 3.6 0.7 - - - +
58A ILE* 3.4 3.6 - - - -
59A SER* 2.7 50.5 + - - +
60A SER 4.3 10.3 - - - +
61A GLY* 5.7 0.4 - - - -
71A ALA* 1.3 79.3 - - - +
73A VAL* 1.3 69.7 + - - +
74A GLN* 4.7 7.9 - - + +
79A ALA* 4.4 16.4 - - + -
80A VAL 3.2 9.4 - - - +
81A MET* 3.8 26.9 - - + -
157A LEU* 4.6 9.2 - - + -
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Residues in contact with VAL 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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56A LEU* 4.2 21.1 - - + -
57A GLU 3.5 3.4 - - - +
58A ILE* 3.8 17.7 - - + -
71A ALA 4.3 0.2 - - - -
72A VAL* 1.3 76.1 - - - +
74A GLN* 1.3 61.0 + - - +
78A THR 4.0 0.9 - - - +
79A ALA* 3.5 1.2 - - - -
80A VAL* 2.9 32.0 + - - +
168A LEU* 3.5 45.7 - - + +
171A ASN* 3.9 8.1 - - + +
172A GLY* 3.5 32.8 - - - +
175A VAL* 4.4 4.5 - - + -
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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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56A LEU* 3.2 5.9 - - - +
57A GLU* 2.8 62.4 + - + +
59A SER* 6.1 0.4 - - - +
72A VAL* 4.1 8.7 - - + +
73A VAL* 1.3 74.5 - - - +
75A SER* 1.3 63.5 + - - +
76A GLY 3.2 22.1 + - - +
77A ASP* 3.8 14.7 + - - +
78A THR 3.4 12.6 - - - +
79A ALA* 3.9 18.1 - - + +
168A LEU* 4.5 0.2 - - - -
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Residues in contact with SER 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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51A LEU* 5.8 0.3 - - - +
54A ARG* 4.6 11.8 - - - +
55A LYS 3.1 21.2 + - - -
56A LEU* 4.0 6.0 - - - +
57A GLU* 5.3 0.7 - - - -
74A GLN* 1.3 75.0 - - - +
76A GLY* 1.3 63.5 + - - +
78A THR* 3.0 19.7 + - - +
163A ASN* 3.4 28.6 + - - +
168A LEU* 3.7 27.4 - - - +
203A ASN* 5.3 2.9 + - - -
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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
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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