Contacts of the strand formed by residues 12 - 18 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLU* 4.1 11.9 + - + +
11A LYS* 1.3 78.5 - - - +
13A TRP* 1.3 62.2 + - - +
14A TYR* 3.2 34.1 + - + +
142A LYS* 3.2 6.0 - - - -
143A ALA 2.7 31.0 + - - -
171A PRO* 3.8 26.6 - - + +
172A LEU 5.4 1.6 - - - +
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Residues in contact with TRP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 1.3 72.0 - - - +
14A TYR* 1.3 65.8 + - - +
45A GLU* 3.9 17.9 - - + -
47A ILE* 3.5 33.2 - - + -
140A LEU* 4.0 25.1 - - + -
141A ILE* 3.2 28.9 - - - -
142A LYS* 3.8 24.1 - - + +
171A PRO* 3.2 9.0 - - - +
172A LEU* 2.8 48.6 + - + +
174A GLU* 2.8 53.7 + - + +
177A VAL* 3.9 31.6 - - + +
178A GLN* 4.7 9.8 - - - +
181A LEU* 4.9 0.4 - - + -
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Residues in contact with TYR 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 3.2 44.2 + - + +
13A TRP* 1.3 79.6 - - - +
15A ALA* 1.3 64.1 + - - +
16A LEU 4.1 0.2 - - - -
140A LEU* 3.5 3.8 - - - +
141A ILE* 2.8 47.8 + - + +
143A ALA* 3.3 18.5 + - + -
145A MET* 3.7 41.8 + - + +
162A PRO* 4.9 7.2 - - + -
169A PRO* 3.9 24.0 - - + -
170A VAL 3.7 6.7 - - - +
171A PRO* 3.7 29.4 - - + -
172A LEU* 3.6 9.8 - - - +
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 1.3 73.7 - - - +
16A LEU* 1.3 57.6 + - - +
17A GLN 4.1 0.2 - - - -
138A TYR* 4.2 5.8 - - + -
139A ILE 3.8 4.9 - - - -
140A LEU* 3.9 15.9 - - + -
162A PRO* 3.1 4.3 - - - +
163A VAL* 2.6 51.8 + - + +
170A VAL 4.7 1.8 + - - -
172A LEU* 3.7 16.6 - - + +
231B ILE* 5.1 0.4 - - + -
232B PHE* 4.1 16.6 - - + -
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 5.0 1.3 - - + -
15A ALA* 1.3 74.9 - - - +
17A GLN* 1.3 61.9 + - - +
18A VAL* 3.6 6.9 + - + +
30A LEU* 3.6 31.0 - - + -
138A TYR* 3.3 9.0 - - - -
139A ILE* 2.9 48.4 + - + +
141A ILE* 3.7 35.7 - - + -
153A ILE* 3.8 20.0 - - + -
159A VAL* 4.4 9.0 - - + -
161A ARG 3.5 3.8 - - - +
162A PRO* 3.7 31.9 - - + -
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Residues in contact with GLN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA 4.1 0.2 + - - -
16A LEU* 1.3 71.5 - - - +
18A VAL* 1.3 62.2 + - - +
137A GLY 3.3 7.4 - - - +
138A TYR* 3.7 22.4 - - + +
159A VAL* 3.9 0.9 - - - +
160A PHE* 2.8 39.5 + - + +
161A ARG* 2.9 32.6 + - - +
162A PRO 4.3 1.7 - - - +
163A VAL* 4.0 17.9 - - + -
164A MET 5.0 0.2 + - - -
206B GLY 5.0 1.0 + - - -
207B PRO* 2.8 50.0 - - - +
209B MET* 5.9 3.6 - - + +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU 3.7 11.2 - - - +
17A GLN* 1.3 81.1 - - - +
19A GLU* 1.3 74.7 + - - +
20A PRO* 3.2 9.4 - - - +
23A GLU* 3.8 25.4 - - + -
26A ALA* 3.8 17.7 - - + -
137A GLY* 2.7 30.8 + - - +
138A TYR* 3.8 2.2 - - - +
139A ILE* 4.2 15.7 - - + -
158A HIS 3.1 14.1 - - - +
159A VAL* 4.1 12.3 - - + -
160A PHE* 3.4 10.6 - - - -
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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