Contacts of the strand formed by residues 79 - 84 (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 VAL 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS 3.6 0.2 - - - -
78A SER* 1.3 91.6 - - - +
80A SER* 1.3 65.7 + - - +
81A VAL 4.5 0.2 - - - +
121A GLU* 3.0 25.8 + - + +
122A VAL* 3.6 16.0 - - + -
123A LYS* 2.8 31.4 + - - +
124A GLU 3.6 3.3 + - - +
174A LEU* 3.5 25.6 - - + +
176A CYS* 3.8 29.2 - - + -
194A LEU* 3.8 21.8 - - + -
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Residues in contact with SER 80 (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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78A SER 4.1 0.4 + - - -
79A VAL* 1.3 70.8 - - - +
81A VAL* 1.3 62.7 + - - +
82A ILE 3.8 0.5 + - - -
123A LYS* 5.1 0.3 - - - +
124A GLU* 2.7 36.8 + - - +
168A ILE* 3.8 23.8 - - - +
172A SER* 3.1 25.1 + - - -
174A LEU 2.9 9.5 + - - -
175A VAL* 3.3 5.9 - - - +
176A CYS 2.8 25.4 + - - -
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Residues in contact with VAL 81 (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* 4.6 0.7 - - + -
80A SER* 1.3 74.5 - - - +
82A ILE* 1.3 69.0 + - - +
83A LEU* 4.1 5.2 - - + +
116A PHE* 3.8 48.0 - - + -
122A VAL* 3.8 28.5 - - + -
124A GLU 2.9 11.6 + - - +
125A ILE* 4.0 13.5 - - + -
126A VAL* 2.7 36.0 + - - +
176A CYS* 3.3 22.2 - - + +
178A HIS* 4.9 0.7 - - + -
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Residues in contact with ILE 82 (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 3.8 0.4 + - - -
81A VAL* 1.3 74.6 - - - +
83A LEU* 1.3 62.0 + - - +
84A LEU* 3.6 14.9 + - + -
126A VAL* 3.5 5.4 - - + -
128A VAL* 3.8 24.5 - - + -
161A VAL* 3.8 20.4 - - + +
164A GLY* 3.7 11.0 - - - +
165A LEU* 3.5 31.9 - - + +
168A ILE* 4.3 9.9 - - + -
175A VAL* 3.5 26.5 - - + -
176A CYS 2.8 10.8 + - - +
177A ILE* 3.5 10.7 - - + +
178A HIS 2.9 27.4 + - - +
245A LEU* 5.2 0.2 - - + -
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Residues in contact with LEU 83 (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* 3.8 3.9 - - + -
82A ILE* 1.3 70.4 - - - +
84A LEU* 1.3 61.8 + - - +
85A ALA* 3.3 2.6 + - + -
109A ALA 4.1 8.7 - - - +
112A SER* 3.6 20.2 - - - +
113A PHE* 3.9 39.9 - - + -
116A PHE* 4.4 6.3 - - + -
125A ILE* 4.1 13.0 - - + -
126A VAL 2.9 14.0 + - - +
127A VAL* 3.7 8.4 - - + +
128A VAL* 2.9 28.5 + - - -
137A PHE* 4.1 13.2 - - + -
178A HIS* 3.7 26.5 - - + +
180A SER* 3.8 17.9 - - - -
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Residues in contact with LEU 84 (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* 4.1 19.7 - - + +
83A LEU* 1.3 68.3 - - - +
85A ALA* 1.3 53.2 + - - +
86A GLY 3.8 1.6 - - - +
128A VAL* 4.2 9.0 - - + -
157A ARG* 3.5 46.3 + - + +
160A SER* 4.0 26.9 - - - -
161A VAL* 4.0 10.5 - - + -
177A ILE* 3.8 25.8 - - + -
178A HIS 2.8 20.5 + - - +
179A ASP* 4.1 6.5 - - + +
180A SER* 2.8 33.0 + - - -
401A PBQ 5.7 0.2 - - + -
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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