Contacts of the strand formed by residues 12 - 18 (chain C) in PDB entry 1NPP
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 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C GLU* 3.7 21.6 + - - +
11C LYS* 1.3 77.9 - - - +
13C TRP* 1.3 65.4 + - - +
14C TYR* 2.9 40.3 - - + +
142C LYS* 3.3 2.4 - - - -
143C ALA 2.8 34.7 + - - -
171C PRO* 3.8 22.9 - - + -
172C LEU 5.9 0.7 - - - +
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Residues in contact with TRP 13 (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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11C LYS 5.5 0.2 - - - -
12C LYS* 1.3 76.5 - - - +
14C TYR* 1.3 63.5 + - - +
45C GLU* 3.9 17.7 - - + -
47C ILE* 3.8 28.0 - - + -
140C LEU* 4.0 26.5 - - + -
141C ILE 3.4 19.3 - - - -
142C LYS* 3.5 40.5 - - + +
171C PRO* 3.2 3.1 - - - +
172C LEU* 2.7 52.8 + - + +
174C GLU* 3.4 41.3 + - + -
177C VAL* 3.7 30.1 - - + -
178C GLN* 5.1 9.0 - - - -
181C LEU* 4.5 1.8 - - + -
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Residues in contact with TYR 14 (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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12C LYS* 2.9 61.4 - - + +
13C TRP* 1.3 78.3 - - - +
15C ALA* 1.3 63.4 + - - +
16C LEU* 5.0 2.9 - - + -
140C LEU* 3.5 4.3 - - - +
141C ILE* 2.9 43.1 + - + -
143C ALA 3.4 18.3 + - - -
145C MET* 4.0 35.5 + - + +
162C PRO* 5.4 1.8 - - + -
169C PRO* 4.1 21.8 - - + -
170C VAL 3.6 9.2 - - - +
171C PRO* 3.4 31.9 - - + -
172C LEU* 3.6 10.3 - - - +
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Residues in contact with ALA 15 (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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14C TYR* 1.3 74.1 - - - +
16C LEU* 1.3 61.4 + - - +
138C TYR* 4.5 3.8 - - + -
139C ILE 3.7 4.7 - - - +
140C LEU* 3.9 16.4 - - + -
162C PRO* 3.4 5.2 - - - +
163C VAL* 2.9 46.2 + - + +
170C VAL 4.7 1.8 + - - -
172C LEU* 3.7 11.3 - - + +
231D ILE* 4.7 1.1 - - + -
232D PHE* 4.0 22.0 - - + -
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Residues in contact with LEU 16 (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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14C TYR* 5.0 1.8 - - + -
15C ALA* 1.3 80.4 - - - +
17C GLN* 1.3 61.6 + - - +
18C VAL* 3.6 6.4 + - + +
30C LEU* 3.8 18.6 - - + -
138C TYR* 3.3 8.9 - - - -
139C ILE* 2.8 46.2 + - + +
141C ILE* 3.5 46.9 - - + -
153C ILE* 4.0 18.2 - - + -
159C VAL* 4.1 14.4 - - + -
161C ARG 3.5 4.5 - - - +
162C PRO* 3.8 28.3 - - + -
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Residues in contact with GLN 17 (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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15C ALA 4.2 0.4 + - - -
16C LEU* 1.3 72.0 - - - +
18C VAL* 1.3 56.3 + - - +
137C GLY 3.4 5.4 - - - +
138C TYR* 3.4 26.2 - - + +
159C VAL* 3.8 0.7 - - - +
160C PHE* 2.8 38.2 + - + +
161C ARG* 2.7 60.0 + - - +
162C PRO 4.5 0.2 + - - -
163C VAL* 4.3 16.0 - - + +
164C MET 5.3 0.2 - - - +
206D GLY 4.6 0.7 - - - -
207D PRO* 2.7 41.8 + - - +
209D MET* 3.9 16.8 - - + +
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Residues in contact with VAL 18 (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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16C LEU 3.6 11.4 - - - +
17C GLN* 1.3 81.4 - - - +
19C GLU* 1.3 73.8 + - - +
20C PRO* 3.1 8.1 - - - +
23C GLU* 4.2 19.5 - - + -
26C ALA* 3.9 18.8 - - + -
137C GLY* 2.9 33.9 + - - +
138C TYR* 3.7 7.0 - - - +
139C ILE* 3.9 15.5 - - + -
158C HIS 3.1 13.0 - - - +
159C VAL* 4.1 12.1 - - + -
160C PHE* 3.8 9.3 - - - +
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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