Contacts of the strand formed by residues 95 - 102 (chain A) in PDB entry 4KG8
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 ALA 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ASN 3.3 7.3 + - - +
94A PRO* 1.3 75.1 - - - +
96A ALA* 1.3 60.5 + - - +
122A PHE* 3.8 14.4 - - + -
124A ARG* 2.7 48.9 + - + +
126A LEU* 3.7 7.1 - - - +
237A ALA 3.1 13.0 - - - +
238A PHE* 3.8 10.8 - - + -
140C TYR* 5.8 3.6 - - + -
206C VAL* 5.4 2.9 - - + -
240C VAL* 4.6 10.5 - - + -
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Residues in contact with ALA 96 (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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95A ALA* 1.3 78.3 - - - +
97A HIS* 1.3 61.9 + - - +
98A LEU* 4.7 1.8 - - + -
122A PHE* 3.3 21.8 - - - +
123A LEU* 4.0 9.4 - - + -
126A LEU* 3.7 17.0 - - + -
133A LEU* 3.9 23.8 - - + -
144A TYR* 3.9 2.9 + - - -
236A GLY* 3.1 2.9 - - - -
237A ALA 2.9 29.9 + - - +
206C VAL* 5.1 1.0 - - - +
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Residues in contact with HIS 97 (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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96A ALA* 1.3 73.0 - - - +
98A LEU* 1.3 61.8 + - - +
99A THR* 3.6 25.5 - - + +
120A LEU* 3.7 18.8 - - + +
121A ALA* 3.1 7.1 - - - -
122A PHE* 2.9 52.4 + - + +
144A TYR* 2.5 26.4 + + - +
230A GLY 5.3 0.4 + - - -
234A TYR* 3.4 45.3 - + + +
235A PHE 3.7 2.7 + - - -
179C LEU 5.2 1.2 + - - -
180C LEU* 4.0 18.8 - - + +
206C VAL 3.6 15.7 + - - +
207C VAL* 5.4 1.5 - - + +
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Residues in contact with LEU 98 (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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96A ALA* 4.9 0.2 - - + -
97A HIS* 1.3 83.1 - - - +
99A THR* 1.3 63.7 + - - +
114A TRP* 3.6 18.8 - - + -
115A GLU 3.6 2.5 - - - +
116A THR* 3.9 27.6 - - + -
122A PHE 3.8 12.8 - - - +
123A LEU* 4.0 12.8 - - + -
128A TYR* 3.7 28.0 - - + -
133A LEU* 3.6 31.2 - - + -
234A TYR* 3.1 8.7 - - - +
235A PHE* 2.6 51.8 + - + +
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Residues in contact with THR 99 (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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97A HIS* 3.6 26.2 - - + +
98A LEU* 1.3 78.1 - - - +
100A GLY* 1.3 63.5 + - - +
114A TRP* 3.5 5.2 - - - -
115A GLU* 2.8 52.5 + - - +
118A LEU 4.7 1.6 + - - -
120A LEU* 4.4 7.9 + - + +
121A ALA* 3.8 20.3 + - + +
230A GLY* 3.1 27.7 - - - +
233A SER 3.6 4.7 - - - -
234A TYR* 4.5 0.7 - - + -
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Residues in contact with GLY 100 (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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99A THR* 1.3 78.8 - - - +
101A ALA* 1.3 66.1 + - - -
102A ASN* 3.4 7.8 + - - -
113A LEU 3.5 6.6 - - - +
114A TRP* 3.9 3.4 - - - -
115A GLU* 4.2 2.3 + - - +
230A GLY* 3.6 22.2 - - - +
233A SER* 3.0 15.9 + - - -
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Residues in contact with ALA 101 (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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100A GLY* 1.3 75.1 - - - +
102A ASN* 1.3 64.9 + - - +
112A LEU* 4.0 19.3 - - + -
113A LEU 3.4 7.4 - - - -
114A TRP* 3.5 29.5 - - + -
147A VAL* 5.2 0.7 - - + -
224A LEU* 4.5 15.7 - - + +
233A SER* 3.8 17.5 - - - +
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Residues in contact with ASN 102 (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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100A GLY 4.3 4.6 + - - -
101A ALA* 1.3 77.5 - - - +
103A SER* 1.3 77.6 + - - +
112A LEU* 3.5 6.9 - - - -
113A LEU* 2.7 53.3 + - - +
224A LEU* 5.0 4.3 - - + -
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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