Contacts of the strand formed by residues 56 - 67 (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 LEU 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C PRO* 1.3 79.5 - - - +
57C GLN* 1.3 66.1 + - - +
58C TYR* 3.2 21.9 + - - +
59C ASN* 5.3 1.2 - - - +
60C TYR* 5.1 1.8 - - + -
88C PHE* 3.7 25.6 - - + -
89C ALA 3.3 11.0 + - - +
90C SER 3.6 36.3 - - - +
91C VAL* 4.0 22.7 - - + -
94C PHE* 5.0 1.3 - - + -
156C LEU* 3.7 39.0 - - + +
52D ILE* 4.1 9.2 - - - +
54D TYR* 4.3 6.3 - - + -
59D LEU* 5.5 0.7 - - + -
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Residues in contact with GLN 57 (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* 1.3 74.9 - - - +
58C TYR* 1.3 87.8 + - + +
60C TYR* 5.8 0.4 - - - -
156C LEU 5.1 2.4 + - - +
158C GLU* 3.6 27.1 - - + +
164C GLU* 5.7 0.2 + - - -
50D THR 4.6 4.9 + - - +
51D ARG* 3.5 38.5 - - - +
52D ILE* 2.9 39.0 + - - +
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Residues in contact with TYR 58 (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* 3.2 24.8 - - - +
57C GLN* 1.3 93.0 - - + +
59C ASN* 1.3 69.8 + - - +
60C TYR* 3.4 32.5 - + + -
88C PHE 4.6 0.2 - - - +
117C LYS* 3.5 37.6 + - + -
158C GLU* 3.1 28.0 - - - -
163C GLY 3.4 6.4 + - - -
164C GLU* 3.0 32.2 + - - -
51D ARG* 2.7 24.6 + - - -
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Residues in contact with ASN 59 (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 5.3 1.4 - - - +
58C TYR* 1.3 80.3 - - - +
60C TYR* 1.3 57.0 + - - +
87C THR* 4.2 5.4 - - + +
88C PHE 3.3 7.9 - - - +
89C ALA* 3.1 32.8 - - - +
117C LYS* 3.4 5.9 - - - -
118C GLU* 2.7 60.2 + - + +
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Residues in contact with TYR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 4.8 3.1 - - + -
57C GLN 5.8 0.2 - - - -
58C TYR* 3.4 47.1 - + + -
59C ASN* 1.3 74.3 - - - +
61C THR* 1.3 62.9 + - - +
87C THR* 3.2 3.7 - - - +
88C PHE* 2.9 58.0 + + + -
115C LEU* 3.7 13.5 - - + -
116C PHE 3.4 7.0 - - - -
117C LYS* 3.6 36.9 - - + +
118C GLU 4.0 0.2 - - - +
155C MET* 3.7 42.4 + - + +
156C LEU* 3.3 30.7 - - + -
158C GLU* 3.8 3.0 + - - -
166C ILE* 5.3 1.6 - - + +
167C CYS 5.1 0.2 - - - -
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Residues in contact with THR 61 (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* 1.3 74.5 - - - +
62C PHE* 1.3 70.3 + - - +
63C TRP* 3.2 30.1 - - + +
84C GLN* 3.8 24.8 + - + +
86C GLY 3.3 12.1 - - - +
87C THR* 2.7 25.9 + - - +
115C LEU* 3.5 5.3 - - - -
116C PHE 2.8 33.6 + - - -
117C LYS 5.3 0.7 - - - -
118C GLU* 3.9 14.9 - - - +
119C GLY 5.0 0.3 + - - -
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Residues in contact with PHE 62 (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 4.3 0.4 + - - -
61C THR* 1.3 80.9 - - - +
63C TRP* 1.3 56.3 + - - +
85C ILE* 2.8 48.8 + - + -
86C GLY 2.8 10.3 + - - +
88C PHE* 3.7 28.5 - + - -
94C PHE* 3.8 26.7 - + - -
97C PHE* 3.9 25.1 - + + -
98C TYR* 4.3 11.2 - + - -
101C MET* 3.8 32.5 - - + -
113C PHE* 5.5 0.2 - - + -
114C HIS 3.3 12.3 - - - -
115C LEU* 3.9 15.5 - - + -
148C TRP* 4.2 24.5 - + - -
152C ILE* 4.6 1.3 - - + -
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Residues in contact with TRP 63 (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* 3.2 34.5 + - + +
62C PHE* 1.3 75.6 - - - +
64C TYR* 1.3 62.8 + - - +
82C ILE* 3.5 25.1 - - + -
83C LYS* 3.2 14.8 - - - +
84C GLN* 3.3 46.4 - - + -
85C ILE* 3.9 5.3 - - - +
113C PHE* 3.5 9.0 - - - +
114C HIS* 2.7 52.2 + - + +
116C PHE* 4.3 6.5 - - + +
119C GLY 6.3 0.4 - - - -
120C ILE 4.2 9.6 + - - -
121C LYS* 4.1 31.0 - - + -
122C PRO* 3.5 27.1 - - + +
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Residues in contact with TYR 64 (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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63C TRP* 1.3 76.6 - - - +
65C SER* 1.3 74.0 + - - +
66C ARG* 3.1 40.3 - - + +
81C ASN 3.5 1.5 - - - +
82C ILE* 4.4 0.2 - - - -
83C LYS* 2.8 60.0 + - + +
85C ILE* 3.7 21.3 - - + -
107C LEU* 4.5 4.0 - - + -
111C SER* 4.2 14.7 + - - -
112C ASP 3.4 13.9 - - - +
113C PHE* 3.9 15.5 - + + -
114C HIS* 4.2 2.5 - - - -
78D ILE* 4.2 9.0 - - + -
81D VAL* 3.4 33.7 - - + +
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Residues in contact with SER 65 (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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64C TYR* 1.3 82.2 - - - +
66C ARG* 1.3 62.5 + - - +
81C ASN* 3.3 18.4 - - - -
82C ILE* 3.7 17.3 - - - -
110C HIS 4.6 0.2 - - - -
111C SER* 3.3 3.5 - - - -
112C ASP* 2.9 43.2 + - - +
114C HIS* 3.1 24.1 + - - -
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Residues in contact with ARG 66 (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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64C TYR* 3.1 31.1 - - + +
65C SER* 1.3 75.5 - - - +
67C ARG* 1.3 70.7 + - - +
81C ASN* 3.6 26.5 + - - +
108C THR* 2.8 47.4 + - - -
109C GLY* 4.1 7.3 - - - -
110C HIS 3.3 8.5 - - - +
111C SER* 3.9 7.2 + - - +
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Residues in contact with ARG 67 (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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66C ARG* 1.3 86.8 + - - +
81C ASN* 4.2 13.5 - - - +
110C HIS* 2.9 67.1 + - + +
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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