Contacts of the strand formed by residues 111 - 117 (chain C) in PDB entry 5NVL
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 SER 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C TYR* 4.2 8.3 + - - -
65C SER 3.3 9.6 - - - -
66C ARG* 3.6 17.0 - - - +
107C LEU* 4.0 26.1 - - - +
108C THR 2.7 26.9 + - - -
109C GLY 3.3 5.5 + - - -
110C HIS* 1.3 74.2 - - - +
112C ASP* 1.3 71.3 + - - +
173C VAL* 2.9 26.0 + - - +
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Residues in contact with ASP 112 (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* 3.5 8.1 - - - -
65C SER* 2.9 42.2 + - - +
107C LEU* 5.3 0.9 - - - -
110C HIS* 4.4 16.6 + - - -
111C SER* 1.3 95.2 + - - +
113C PHE* 1.3 64.5 + - - +
114C HIS* 3.4 27.2 + - + +
170C VAL* 4.4 1.8 - - + -
171C VAL 3.3 7.6 - - - +
172C SER* 3.1 30.6 + - - +
173C VAL 3.8 0.5 + - - -
174C ARG* 4.7 4.9 + - - -
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Residues in contact with PHE 113 (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* 5.2 1.3 - - + -
63C TRP 3.5 4.9 - - - +
64C TYR* 3.4 29.2 - + + -
101C MET* 3.7 34.3 - - + -
102C VAL 3.2 27.1 - - - -
104C PRO* 4.1 22.9 - - + -
107C LEU* 3.9 28.8 - - + +
112C ASP* 1.3 80.0 - - - +
114C HIS* 1.3 60.5 + - - +
148C TRP* 4.0 17.6 - - + -
170C VAL* 3.4 5.5 - - - +
171C VAL* 3.0 42.3 + - + +
70D ILE* 4.0 15.3 - - + -
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Residues in contact with HIS 114 (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 3.6 0.6 - - - +
62C PHE* 3.3 7.4 - - - -
63C TRP* 2.7 55.5 + - + +
64C TYR 4.4 0.2 - - - -
65C SER* 3.4 9.8 + - - -
82C ILE* 3.3 32.3 - - + +
112C ASP* 3.4 33.5 - - + +
113C PHE* 1.3 77.5 - - - +
115C LEU* 1.3 60.1 + - - +
116C PHE* 3.8 16.2 - - + -
122C PRO* 4.1 15.6 + - + +
148C TRP* 4.7 0.2 - - - -
169C ALA 3.6 4.3 - - - -
170C VAL* 3.5 21.2 - - + +
183C TRP* 6.1 0.7 - + - -
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Residues in contact with LEU 115 (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* 3.8 10.5 - - + -
61C THR 3.4 15.5 - - - +
62C PHE* 4.0 24.7 - - + -
88C PHE* 3.6 30.7 - - + -
94C PHE* 4.7 0.2 - - + -
114C HIS* 1.3 73.9 - - - +
116C PHE* 1.3 57.4 + - - +
148C TRP* 4.0 13.7 - - + -
152C ILE* 3.8 24.7 - - + -
155C MET* 3.6 25.5 - - + +
156C LEU* 4.2 15.0 - - + -
168C GLY* 3.1 2.8 - - - -
169C ALA 2.8 36.2 + - - -
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Residues in contact with PHE 116 (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* 3.3 7.5 - - - -
61C THR* 2.8 33.4 + - - +
63C TRP* 4.7 6.5 - + - +
114C HIS* 3.8 2.9 - - + -
115C LEU* 1.3 82.0 - - - +
117C LYS* 1.3 63.8 + - - +
120C ILE* 3.7 33.9 - - + +
122C PRO* 3.7 26.9 - - + -
167C CYS* 3.4 22.2 - - + -
168C GLY* 3.8 9.9 - - - -
169C ALA 3.6 6.7 - - - -
170C VAL* 3.5 23.8 - - + -
183C TRP* 3.4 56.3 - + + -
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Residues in contact with LYS 117 (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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58C TYR* 3.6 54.7 - - + -
59C ASN 3.5 7.6 - - - +
60C TYR* 3.8 23.9 - - + -
61C THR* 4.9 1.2 + - - -
116C PHE* 1.3 74.5 - - - +
118C GLU* 1.3 70.6 + - - +
119C GLY 3.3 0.3 + - - -
120C ILE* 3.1 36.3 + - + +
158C GLU* 5.3 0.7 - - - -
163C GLY 4.7 1.0 + - - -
164C GLU* 3.2 22.2 + - - +
166C ILE* 2.6 36.8 + - - +
167C CYS 2.9 17.2 + - - +
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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