Contacts of the strand formed by residues 97 - 109 (chain A) in PDB entry 4KXA
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 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PRO* 3.9 21.4 + - + +
96A PHE* 1.3 99.7 - - + +
98A ASN* 1.3 60.4 + - - +
99A PRO* 4.4 1.3 - - - +
123A ILE* 3.5 25.8 - - + -
124A ASN 3.8 1.8 - - - -
125A LEU* 4.8 5.6 - - + +
132A LEU* 4.4 24.9 - - + -
133A TRP* 5.4 6.7 - - + +
234A PHE* 3.8 27.9 - - + -
239A LYS* 3.0 25.3 + - - +
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Residues in contact with ASN 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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95A ASP 3.5 17.8 - - - +
96A PHE 4.7 1.0 - - - -
97A VAL* 1.3 83.1 + - - +
99A PRO* 1.3 77.0 + - - +
100A VAL* 5.9 0.4 - - + -
123A ILE* 3.3 4.6 - - - -
124A ASN* 2.6 53.3 + - + +
234A PHE* 5.4 0.2 - - - -
238A ASN 4.9 3.6 + - - -
239A LYS* 3.8 20.2 + - - +
240A LYS 5.6 1.4 + - - +
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Residues in contact with PRO 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A VAL 4.4 0.9 - - - +
98A ASN* 1.3 98.7 + - + +
100A VAL* 1.3 62.3 + - - +
102A TYR* 3.8 20.0 - - + +
121A ILE* 4.0 7.0 - - + -
122A SER 3.4 6.5 - - - +
123A ILE* 4.5 1.6 - - + -
234A PHE* 3.8 34.7 - - + -
239A LYS* 3.7 36.1 - - + +
240A LYS 3.6 13.2 - - - +
241A ALA* 4.0 3.6 - - + -
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASN* 5.2 0.4 - - + -
99A PRO* 1.3 77.5 - - - +
101A HIS* 1.3 62.2 - - + +
122A SER* 2.7 22.7 + - - +
124A ASN* 4.4 13.0 - - + +
185A LEU* 3.9 34.1 - - + -
240A LYS 5.2 0.2 - - - -
241A ALA* 3.4 5.8 - - - +
242A THR* 2.8 34.4 + - + +
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Residues in contact with HIS 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 VAL* 1.3 80.0 - - + +
102A TYR* 1.3 94.1 + - - +
103A ASP* 3.7 16.1 + - - -
120A SER 3.6 1.4 + - - +
121A ILE* 3.3 7.1 - - - +
122A SER* 2.8 46.4 + - - +
242A THR* 3.2 33.0 + - + -
243A TYR 4.3 0.4 - - - -
244A THR* 3.2 37.1 + - + +
278A LYS* 5.0 4.8 - - + +
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PRO* 3.8 10.3 - - + +
101A HIS* 1.3 82.6 + - - +
103A ASP* 1.3 59.5 + - - +
104A LEU* 3.8 3.0 + - + +
119A VAL* 3.9 13.5 - - + -
120A SER 3.4 3.4 - - - -
121A ILE* 3.8 32.8 - - + -
231A PHE* 4.2 5.4 - + - -
232A PRO 4.2 0.9 - - - -
233A CYS* 3.5 19.8 - - + +
234A PHE* 2.8 41.1 + - - +
239A LYS 5.2 0.4 - - - -
241A ALA* 3.5 24.2 - - + -
242A THR 2.8 8.5 + - - -
243A TYR* 3.4 50.8 - + + +
244A THR 3.1 27.2 + - - +
284A THR* 4.3 3.9 - - + +
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Residues in contact with ASP 103 (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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101A HIS* 3.7 14.3 + - - -
102A TYR* 1.3 70.2 - - - +
104A LEU* 1.3 60.4 + - - +
105A HIS 4.2 0.2 - - - -
118A THR 3.8 1.4 - - - +
119A VAL* 3.3 5.4 - - - -
120A SER* 2.7 54.6 + - - +
187A LEU* 6.0 1.4 - - - +
244A THR* 2.7 27.1 + - - +
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Residues in contact with LEU 104 (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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102A TYR* 3.8 6.5 - - + +
103A ASP* 1.3 73.8 - - - +
105A HIS* 1.3 62.0 + - - +
106A VAL* 4.1 12.1 - - + +
118A THR 3.9 0.2 - - - -
119A VAL* 4.1 14.8 - - + -
192A PHE* 3.9 16.2 - - + -
231A PHE* 3.7 58.8 - - + -
243A TYR* 5.2 2.5 - - + -
244A THR 3.2 7.9 + - - +
245A ILE* 3.5 25.2 - - + -
246A SER* 2.9 28.8 + - - +
287A VAL* 4.7 2.5 - - + -
289A PHE* 4.1 16.4 - - + -
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Residues in contact with HIS 105 (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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103A ASP 4.1 0.4 + - - -
104A LEU* 1.3 73.2 - - - +
106A VAL* 1.3 67.0 + - - +
107A LYS* 4.1 12.8 - - + +
117A GLY* 2.9 26.9 - - - -
118A THR* 3.0 35.0 + - + +
192A PHE* 4.3 0.7 - - - -
246A SER* 3.1 29.0 + - - +
248A THR* 2.9 43.8 + - - -
273A ARG* 3.1 23.9 + - + +
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Residues in contact with VAL 106 (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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104A LEU* 4.1 19.3 - - + -
105A HIS* 1.3 81.7 - - - +
107A LYS* 1.3 60.4 + - - +
108A PRO* 4.0 0.7 - - + -
115A TYR* 4.6 7.4 - - + -
116A THR 3.3 7.6 - - - +
192A PHE* 4.3 15.0 - - + -
203A PHE* 4.5 13.0 - - + -
230A SER 5.5 0.2 - - - +
231A PHE* 5.5 1.1 - - + -
245A ILE* 5.6 1.1 - - + -
246A SER 3.2 4.2 + - - +
247A ILE* 3.3 26.9 - - + +
248A THR 3.1 22.0 + - - -
289A PHE* 3.9 37.7 - - + -
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Residues in contact with LYS 107 (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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105A HIS* 4.1 9.2 + - + +
106A VAL* 1.3 74.3 - - - +
108A PRO* 1.3 64.2 - - - +
109A LEU* 3.8 18.0 + - + +
115A TYR* 3.3 2.7 - - - -
116A THR* 2.7 45.8 + - - +
248A THR* 3.5 35.0 - - + +
271A TRP* 3.8 39.5 - - + +
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Residues in contact with PRO 108 (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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106A VAL 3.8 5.6 - - - +
107A LYS* 1.3 87.2 - - - +
109A LEU* 1.3 60.3 + - - +
110A LEU* 3.5 29.2 + - + +
114A THR 3.6 5.4 - - - +
115A TYR* 3.7 4.2 - - + -
196A LEU* 4.3 5.4 - - + -
203A PHE* 4.2 22.9 - - + -
247A ILE* 4.1 7.4 - - + -
248A THR 3.2 15.5 - - - +
249A HIS* 4.8 4.9 - - + -
250A PRO* 4.8 1.5 - - + +
271A TRP* 3.6 21.5 - - - -
291A VAL* 4.4 20.9 - - + -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 3.8 32.9 + - + +
108A PRO* 1.3 72.1 - - - +
110A LEU* 1.3 54.6 + - - +
111A GLU 3.3 2.2 - - - -
112A GLU* 2.8 48.2 + - + +
113A ASP 3.1 9.5 + - - -
114A THR* 2.7 33.6 + - - +
115A TYR* 5.5 0.9 - - - -
116A THR* 5.9 1.1 - - - +
271A TRP* 4.0 12.6 - - + -
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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