Contacts of the strand formed by residues 174 - 179 (chain A) in PDB entry 4NAK
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 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A SER* 3.4 3.2 + - - +
79A VAL* 3.5 20.8 - - + -
80A SER* 2.9 27.9 + - - +
172A SER* 3.4 5.5 + - - -
173A GLU* 1.3 89.4 - - + +
175A VAL* 1.3 63.1 + - - +
194A LEU* 3.5 35.9 - - + +
197A GLY 3.9 17.0 - - - +
198A SER* 3.9 14.1 - - - +
239A VAL* 3.5 24.5 - - + -
240A ILE 3.9 2.2 - - - -
241A LYS* 3.8 25.6 - - + +
242A PRO* 3.8 0.9 - - - +
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Residues in contact with VAL 175 (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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80A SER 3.3 7.2 - - - +
82A ILE* 3.5 33.7 - - + -
165A LEU* 4.4 6.3 - - + -
168A ILE* 3.8 28.3 - - + -
174A LEU* 1.3 75.7 - - - +
176A CYS* 1.3 61.7 + - - +
177A ILE* 4.1 12.3 - - + -
238A GLN 3.8 1.7 - - - +
239A VAL* 3.3 6.1 - - - +
240A ILE* 2.7 49.9 + - + +
242A PRO* 3.9 18.6 - - + -
245A LEU* 4.3 8.5 - - + -
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Residues in contact with CYS 176 (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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79A VAL* 3.8 22.2 - - + -
80A SER 2.8 10.9 + - - +
81A VAL* 3.3 13.4 - - + +
82A ILE 2.8 27.0 + - - -
116A PHE* 3.9 20.4 - - - -
122A VAL* 6.4 0.2 - - - -
174A LEU 4.1 0.2 + - - -
175A VAL* 1.3 71.9 - - - +
177A ILE* 1.3 56.8 + - - +
190A VAL* 4.8 2.0 - - - -
194A LEU* 4.1 13.0 - - + -
237A PRO* 3.6 33.7 - - - -
238A GLN 3.9 2.5 - - - -
239A VAL* 4.2 7.2 - - + -
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Residues in contact with ILE 177 (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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82A ILE* 3.5 12.1 - - + +
84A LEU* 3.8 26.9 - - + -
161A VAL* 3.8 35.0 - - + -
175A VAL* 4.1 14.8 - - + +
176A CYS* 1.3 70.6 - - - +
178A HIS* 1.3 63.6 + - - +
236A THR* 3.8 5.8 - - + -
237A PRO* 3.2 4.3 - - - +
238A GLN* 2.9 56.9 + - + +
240A ILE* 4.3 19.1 - - + -
245A LEU* 4.5 4.7 - - + -
401A PBQ 4.5 22.2 - - + -
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Residues in contact with HIS 178 (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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81A VAL* 4.9 0.4 - - + -
82A ILE 2.9 11.4 + - - +
83A LEU* 3.6 7.9 - - + +
84A LEU* 2.8 36.7 + - - +
112A SER* 3.4 28.5 - - - -
116A PHE* 3.6 24.9 - + + -
176A CYS 3.7 2.4 + - - +
177A ILE* 1.3 77.3 - - - +
179A ASP* 1.3 71.8 + - - +
180A SER 3.4 0.5 + - - -
182A ARG* 2.8 35.4 + - + -
185A VAL* 3.8 15.7 - - + +
236A THR* 2.8 35.1 + - - -
237A PRO* 3.4 14.4 - - + +
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Residues in contact with ASP 179 (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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84A LEU* 4.1 11.3 - - + +
157A ARG* 2.9 40.1 + - - +
178A HIS* 1.3 81.9 + - - +
180A SER* 1.3 59.7 + - - +
181A ALA* 3.0 23.1 + - - +
182A ARG* 2.9 27.9 + - + +
236A THR* 3.1 26.7 + - + +
284A LYS* 3.3 22.0 + - - +
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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