Contacts of the strand formed by residues 83 - 90 (chain C) in PDB entry 5NVN
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 LYS 83 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C TRP* 3.2 10.5 - - - -
64C TYR* 2.8 60.6 + - + +
81C ASN 4.5 4.0 - - - +
82C ILE* 1.3 75.4 - - - +
84C GLN* 1.3 65.5 + - - +
85C ILE 3.7 0.2 + - - -
76D PRO* 5.8 2.0 - - + +
77D THR 5.6 0.2 + - - -
78D ILE* 3.4 45.4 - - + +
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Residues in contact with GLN 84 (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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61C THR* 3.8 18.6 + - + +
62C PHE 3.7 3.8 - - - +
63C TRP* 3.3 44.4 - - + -
83C LYS* 1.3 79.4 - - - +
85C ILE* 1.3 62.5 + - - +
86C GLY* 4.7 4.8 - - - +
87C THR* 4.3 6.6 + - - -
76D PRO* 4.0 11.1 - - - +
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Residues in contact with ILE 85 (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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62C PHE* 2.8 22.9 + - + +
63C TRP 3.9 9.4 - - - +
64C TYR* 3.7 31.0 - - + -
83C LYS 4.4 0.4 - - - +
84C GLN* 1.3 75.9 - - - +
86C GLY* 1.3 56.5 + - - +
97C PHE* 3.8 13.2 - - + -
101C MET* 3.6 33.2 - - + -
74D ASP* 4.0 4.5 - - - +
75D LEU* 3.8 24.0 - - + -
76D PRO* 3.0 27.3 - - + +
78D ILE* 4.4 13.2 - - + -
81D VAL* 4.3 9.6 - - + -
82D THR* 4.0 10.3 - - + -
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Residues in contact with GLY 86 (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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60C TYR 4.0 0.3 - - - +
61C THR* 3.3 5.1 - - - +
62C PHE* 2.8 28.5 + - - +
84C GLN* 3.8 5.0 - - - -
85C ILE* 1.3 82.5 - - - +
87C THR* 1.3 63.9 + - - -
88C PHE* 4.6 2.4 - - - -
97C PHE* 3.6 18.8 - - - -
74D ASP* 5.7 4.3 - - - -
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Residues in contact with THR 87 (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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59C ASN* 4.2 6.3 - - + +
60C TYR 3.2 15.7 - - - +
61C THR* 2.7 24.9 + - - +
84C GLN* 4.3 6.2 + - - -
86C GLY* 1.3 74.5 - - - -
88C PHE* 1.3 70.6 + - - +
93C GLN* 5.0 2.4 + - - -
97C PHE* 3.7 11.5 - - - -
118C GLU* 3.8 31.5 + - + +
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Residues in contact with PHE 88 (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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56C LEU* 3.7 22.2 - - + -
58C TYR 4.6 0.2 - - - +
59C ASN* 3.3 6.9 - - - +
60C TYR* 2.9 60.4 + - + -
61C THR 4.6 0.2 - - - -
62C PHE* 3.7 25.8 - + - -
86C GLY 4.6 1.1 - - - -
87C THR* 1.3 80.7 - - - +
89C ALA* 1.3 60.7 + - - +
90C SER 3.9 1.3 - - - -
93C GLN* 3.7 24.2 - - + +
94C PHE* 3.5 43.5 - + + +
97C PHE* 4.1 18.2 - + + -
115C LEU* 3.7 14.6 - - + -
156C LEU* 4.0 8.1 - - + -
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Residues in contact with ALA 89 (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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55C PRO* 3.8 4.9 - - - +
56C LEU* 3.3 26.2 + - - +
59C ASN* 3.1 31.5 - - - +
88C PHE* 1.3 73.7 - - - +
90C SER* 1.3 62.0 + - - +
93C GLN* 4.5 3.8 - - - +
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Residues in contact with SER 90 (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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53C GLU* 2.7 40.0 + - - -
54C HIS 3.2 17.0 - - - -
55C PRO* 4.6 0.9 - - - -
56C LEU* 3.6 14.4 - - - +
88C PHE* 3.9 0.5 - - - -
89C ALA* 1.3 79.6 - - - +
91C VAL* 1.3 65.5 + - - +
92C GLU* 3.7 0.7 + - - -
93C GLN* 3.2 18.0 + - - +
94C PHE* 3.0 18.9 + - - +
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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