Contacts of the strand formed by residues 88 - 99 (chain A) in PDB entry 3D5K
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 ILE 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A PRO* 3.8 15.3 - - + +
87A ARG* 1.3 73.2 - - - +
89A GLY* 1.3 59.7 + - - +
119A LEU* 4.0 30.1 - - + -
120A GLY* 3.5 12.8 - - - +
121A THR* 3.6 15.9 - - - +
333B PRO* 4.0 1.3 - - - +
334B ILE* 2.9 10.3 + - + +
335B PHE* 2.7 63.4 + - + +
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Residues in contact with GLY 89 (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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87A ARG 3.8 1.6 + - - -
88A ILE* 1.3 75.1 - - - +
90A VAL* 1.3 64.8 + - - -
91A ASP* 3.9 1.5 + - - +
119A LEU* 3.4 9.6 - - - +
120A GLY 3.2 31.5 + - - +
331B ASN* 4.6 9.6 - - - -
332B LEU 3.4 12.1 - - - -
333B PRO* 4.1 3.8 - - - -
334B ILE* 3.8 5.8 - - - -
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLY* 1.3 72.8 - - - -
91A ASP* 1.3 62.0 + - - +
92A GLY* 4.9 1.3 - - - +
117A VAL* 4.3 19.1 - - + -
118A THR 3.3 10.1 - - - +
119A LEU* 4.1 11.4 - - + -
330B ILE 3.6 1.6 - - - +
331B ASN* 3.3 6.3 + - - -
332B LEU* 2.8 48.6 + - + +
334B ILE* 3.8 26.0 - - + -
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Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLY 3.9 2.8 + - - +
90A VAL* 1.3 72.7 - - - +
92A GLY* 1.3 65.5 + - - +
93A SER* 4.1 9.9 + - - -
116A GLY 3.5 4.2 - - - +
117A VAL* 4.6 0.2 - - - -
118A THR* 2.9 51.4 + - + +
120A GLY 6.1 0.2 - - - +
329B SER* 5.5 5.2 - - - -
330B ILE 3.5 3.8 - - - +
331B ASN* 3.1 32.9 + - - +
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Residues in contact with GLY 92 (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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90A VAL* 4.0 3.6 + - - +
91A ASP* 1.3 74.9 - - - +
93A SER* 1.3 60.9 + - - -
116A GLY 3.3 7.0 - - - -
117A VAL* 4.4 12.1 - - - -
329B SER* 3.5 2.8 - - - -
330B ILE* 2.8 53.3 + - - +
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Residues in contact with SER 93 (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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91A ASP* 4.7 10.6 + - - -
92A GLY* 1.3 75.9 - - - -
94A GLY* 1.3 61.3 + - - +
95A THR* 5.5 2.0 + - - -
114A GLN 4.7 0.2 - - - -
115A TYR* 3.4 7.3 - - - +
116A GLY* 2.9 37.6 + - - +
309A MET* 5.9 2.3 - - - +
328B PRO 3.7 7.6 - - - -
329B SER* 4.8 5.8 - - - -
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Residues in contact with GLY 94 (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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93A SER* 1.3 74.4 - - - +
95A THR* 1.3 67.4 + - - -
114A GLN 3.5 4.9 - - - -
115A TYR* 4.0 16.2 - - - -
327B GLN* 3.4 22.0 - - - +
328B PRO* 3.1 27.5 + - - +
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Residues in contact with THR 95 (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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93A SER* 5.3 2.6 + - - -
94A GLY* 1.3 79.3 + - - -
96A ARG* 1.3 65.8 + - - +
97A GLN* 5.1 8.1 - - + -
112A SER 5.9 0.7 - - - +
113A SER* 3.3 8.6 + - - -
114A GLN* 2.9 52.3 + - + +
115A TYR* 4.8 4.8 - - - -
325B LEU* 4.3 9.9 - - + -
326B PHE 3.5 5.1 + - - -
327B GLN* 3.7 28.8 + - - +
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Residues in contact with ARG 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 THR* 1.3 77.4 - - - +
97A GLN* 1.3 61.5 + - - +
111A ILE* 4.1 28.7 - - + +
112A SER 3.6 4.9 - - - +
113A SER* 3.6 22.2 + - - +
115A TYR* 4.1 16.4 + - - +
324B TRP* 3.7 18.2 + - - +
325B LEU* 3.6 1.6 - - - -
326B PHE* 2.9 51.7 + - + +
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Residues in contact with GLN 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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95A THR* 4.3 7.8 - - + -
96A ARG* 1.3 75.4 - - - +
98A ARG* 1.3 62.1 + - - +
99A LEU* 3.7 34.0 + - + +
111A ILE* 3.4 5.3 - - - -
112A SER* 2.9 45.3 + - - +
309B MET* 4.4 11.7 - - - +
324B TRP* 3.2 17.8 - - - +
325B LEU* 3.8 23.7 - - + +
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Residues in contact with ARG 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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97A GLN* 1.3 73.2 - - - +
99A LEU* 1.3 67.3 + - - +
100A PRO* 6.0 0.2 - - - +
109A PRO* 4.0 27.8 - - - +
110A ALA 3.5 7.9 - - - +
111A ILE* 3.9 21.8 - - + -
309B MET* 4.2 3.5 - - - +
320B GLY* 5.6 6.9 + - - -
322B GLY* 4.1 25.4 + - - +
323B SER* 3.4 22.7 - - - +
324B TRP* 3.4 53.8 + - + +
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Residues in contact with LEU 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 GLN* 3.7 28.7 - - + +
98A ARG* 1.3 80.4 - - - +
100A PRO* 1.3 70.2 - - + +
103A LEU* 4.1 28.3 - - + +
104A SER* 4.2 14.4 - - - +
109A PRO* 3.4 3.1 - - - +
110A ALA* 2.8 38.3 + - + +
112A SER* 3.8 18.8 - - - +
114B GLN* 5.9 3.4 - - - +
309B MET* 3.7 24.9 - - + -
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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