Contacts of the strand formed by residues 69 - 74 (chain A) in PDB entry 5V5W
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 GLN 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 ARG 3.5 3.0 + - - -
68A PRO* 1.3 73.1 - - - +
70A VAL* 1.3 63.9 - - - +
71A ARG* 3.5 30.2 + - + +
88A VAL* 3.3 36.4 - - + +
109A LYS 3.6 0.9 - - - +
110A ALA* 3.2 6.4 - - - -
111A GLU* 2.8 48.9 + - + +
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Residues in contact with VAL 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 CYS* 3.9 14.6 - - + +
62A VAL* 3.7 30.3 - - + -
68A PRO 3.8 7.9 - - - +
69A GLN* 1.3 80.4 - - - +
71A ARG* 1.3 65.7 + - - +
72A TRP* 4.6 4.3 - - + +
88A VAL* 3.5 7.5 - - - +
89A PHE 3.1 23.8 + - - -
90A ASN* 4.1 2.9 + - - +
91A GLU* 3.9 30.1 - - + +
108A CYS* 3.8 23.8 - - - -
109A LYS 3.4 2.7 - - - +
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 3.5 14.5 - - + +
70A VAL* 1.3 79.0 - - - +
72A TRP* 1.3 64.0 + - - +
86A THR* 2.8 39.3 + - - -
87A SER 3.1 23.7 - - - +
88A VAL* 3.6 22.4 - - + +
89A PHE 4.6 0.4 - - - +
107A TYR 3.7 0.2 - - - +
108A CYS* 3.3 8.1 - - - -
109A LYS* 2.7 57.2 + - + +
111A GLU* 2.9 28.2 + - - +
302A SO4 2.7 44.9 + - - -
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Residues in contact with TRP 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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29A ILE* 4.0 16.2 - - + -
58A LEU* 3.8 41.3 - - + -
59A GLN 4.2 1.3 - - - -
60A CYS* 4.0 18.4 - - + +
70A VAL* 4.6 2.4 - - + +
71A ARG* 1.3 76.3 - - - +
73A THR* 1.3 69.0 + - - +
86A THR* 3.6 2.6 - - - -
87A SER* 3.2 28.7 + - - +
89A PHE* 3.7 40.0 - + + +
91A GLU 2.9 22.1 + - - -
93A LEU* 3.7 29.6 - - + +
106A TYR* 3.9 26.2 - + + -
107A TYR 3.2 39.5 - - - -
108A CYS* 3.8 14.1 - - + -
122A ILE* 5.0 0.2 - - + -
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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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72A TRP* 1.3 80.1 - - - +
74A LYS* 1.3 69.2 + - - +
75A THR* 6.0 0.2 - - - -
84A GLN* 4.4 10.4 + - + +
85A GLU 3.3 27.5 + - - -
86A THR* 4.0 17.5 - - + -
87A SER* 5.8 0.4 - - - -
106A TYR* 3.5 9.2 - - - -
107A TYR* 3.0 55.9 + - + +
109A LYS* 6.5 1.6 - - + -
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Residues in contact with LYS 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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73A THR* 1.3 80.8 + - - +
75A THR* 1.3 79.8 + - - +
76A ALA* 2.8 31.9 + - + +
84A GLN* 4.4 4.7 - - - +
101A THR 5.1 3.8 - - - -
102A GLN* 4.4 4.5 - - - +
103A GLY 3.0 30.3 + - - -
104A GLY* 4.1 4.8 - - - -
105A ARG 3.7 15.7 - - - +
106A TYR* 3.7 33.9 - - + +
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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