Contacts of the strand formed by residues 73 - 80 (chain C) in PDB entry 5VXZ
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 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A LYS 3.5 4.5 - - - -
313A ARG* 3.6 20.2 - - - +
314A LEU* 2.9 45.0 + - + +
315A GLN* 4.9 1.4 + - - +
72C VAL* 1.3 70.6 - - - +
74C SER* 1.3 56.9 + - - +
94C GLN 3.9 0.2 - - - +
95C LEU* 3.5 5.3 - - - +
96C ARG* 2.9 53.9 + - + +
98C THR* 3.2 23.6 + - - -
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ARG 4.0 0.7 + - - +
311A PHE* 3.6 0.7 - - - -
312A LYS* 2.9 51.0 + - - +
313A ARG* 2.8 21.8 + - - -
60C VAL 5.7 0.9 + - - -
62C TRP* 4.3 19.1 - - - -
72C VAL* 3.5 16.9 + - - -
73C ASP* 1.3 74.6 - - - +
75C THR* 1.3 56.8 + - - +
76C GLN* 4.2 3.3 + - - +
93C SER* 4.4 4.7 + - - -
94C GLN 3.2 9.6 - - - -
95C LEU* 4.6 0.9 - - - -
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Residues in contact with THR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A LEU* 4.8 9.0 - - + -
310A ARG 3.6 3.4 - - - +
311A PHE* 3.4 27.8 - - + -
313A ARG* 3.0 23.4 + - - +
455A ASP* 5.1 16.1 - - + +
74C SER* 1.3 70.4 - - - +
76C GLN* 1.3 66.2 + - - +
77C THR* 4.7 4.6 + - - +
92C ALA 4.0 0.2 - - - +
93C SER* 3.3 4.4 - - - -
94C GLN* 2.8 46.7 + - - +
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Residues in contact with GLN 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ARG 3.7 0.6 - - - +
309A LEU* 3.2 8.5 - - - +
310A ARG* 2.9 62.1 + - + +
58C PRO 4.6 0.9 - - - -
59C GLU* 3.6 15.6 - - - +
60C VAL* 2.9 42.0 + - + +
74C SER* 4.2 3.7 - - - +
75C THR* 1.3 72.8 - - - +
77C THR* 1.3 67.0 + - - +
78C GLN* 3.2 30.8 - - + +
91C VAL* 4.5 4.7 - - + -
92C ALA 3.3 10.8 - - - +
93C SER* 4.3 6.4 + - - +
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Residues in contact with THR 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ILE* 4.5 2.2 - - + -
308A ARG 3.4 4.3 - - - +
309A LEU* 3.5 21.9 - - + +
455A ASP* 4.0 15.6 + - - -
457A THR* 4.2 21.8 + - + -
458A ILE* 4.3 13.6 - - + +
75C THR* 4.7 5.4 + - - +
76C GLN* 1.3 75.9 - - - +
78C GLN* 1.3 66.6 + - - +
79C VAL* 4.1 20.2 - - + -
90C ILE* 3.6 1.5 - - + +
91C VAL* 3.3 5.7 - - - +
92C ALA* 2.8 38.3 + - - +
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Residues in contact with GLN 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ILE* 3.8 1.7 - - - +
308A ARG* 2.7 63.9 + - + +
57C PRO* 3.7 31.0 + - + +
58C PRO 3.6 16.4 + - - -
59C GLU* 5.1 0.2 - - - +
76C GLN* 3.2 28.8 - - + +
77C THR* 1.3 78.3 - - - +
79C VAL* 1.3 64.6 + - - +
80C PRO* 4.1 2.1 - - - +
89C TRP* 3.8 15.9 - - + -
90C ILE 3.2 5.2 - - - +
91C VAL* 4.4 6.3 - - + -
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Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ARG* 4.3 0.7 - - - +
306A VAL 3.8 13.2 - - - +
307A ILE* 3.5 20.2 - - + -
457A THR* 5.4 0.2 - - + -
458A ILE* 5.5 1.8 - - + -
461A THR* 4.2 19.5 - - + +
468A MET* 3.9 33.7 - - + -
77C THR* 4.1 15.3 - - + -
78C GLN* 1.3 75.1 - - - +
80C PRO* 1.3 73.0 - - + +
81C LEU* 3.4 4.6 + - + +
89C TRP* 3.3 3.8 - - - -
90C ILE* 2.8 50.4 + - + +
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Residues in contact with PRO 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ARG* 2.9 30.7 + - - +
300A MET* 4.0 27.4 - - + -
304A THR* 5.3 0.9 - - + -
305A PRO 3.8 18.4 - - - +
306A VAL 3.3 21.5 - - - +
307A ILE* 4.6 0.4 - - - +
308A ARG* 5.4 0.4 - - - +
78C GLN 4.1 1.1 - - - +
79C VAL* 1.3 84.7 - - - +
81C LEU* 1.3 58.6 + - - +
82C GLY 3.6 2.0 - - - +
84C ASP 5.1 4.0 - - - +
85C GLU* 5.5 0.2 - - + -
88C ASP 3.8 1.8 - - - +
89C TRP* 3.4 43.2 - - + +
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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