Contacts of the strand formed by residues 88 - 99 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B PRO* 3.5 20.2 + - + +
87B ARG* 1.3 77.9 - - - +
89B GLY* 1.3 60.4 + - - +
119B LEU* 4.1 24.0 - - + -
120B GLY* 3.5 18.6 - - - +
121B THR* 4.9 1.8 - - - -
333C PRO* 4.3 0.7 - - - +
334C ILE* 2.9 11.5 + - + +
335C PHE* 2.6 68.7 + - + +
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Residues in contact with GLY 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG 3.9 1.0 + - - -
88B ILE* 1.3 75.8 - - - +
90B VAL* 1.3 64.8 + - - -
91B ASP* 4.0 3.7 + - - +
118B THR 3.8 0.5 - - - +
119B LEU* 3.4 6.7 - - - +
120B GLY 3.0 33.8 + - - +
331C ASN* 4.6 7.6 - - - -
332C LEU 3.3 12.1 - - - -
333C PRO* 4.2 2.9 - - - -
334C ILE* 3.7 5.4 - - - -
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLY* 1.3 73.4 - - - -
91B ASP* 1.3 63.9 + - - +
92B GLY 4.1 1.1 + - - +
117B VAL* 4.3 20.4 - - + -
118B THR 3.3 11.0 - - - +
119B LEU* 3.8 13.9 - - + -
330C ILE 3.6 1.2 - - - +
331C ASN* 3.3 5.8 + - - -
332C LEU* 2.7 49.9 + - + +
334C ILE* 3.6 27.8 - - + -
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Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLY 4.4 6.6 - - - +
90B VAL* 1.3 73.5 - - - +
92B GLY* 1.3 60.8 + - - +
93B SER* 4.0 5.2 + - - +
116B GLY 3.5 2.4 - - - +
117B VAL* 3.4 3.0 - - - -
118B THR* 2.9 52.3 + - + +
120B GLY 4.8 6.4 + - - +
122B THR* 4.1 16.6 + - - -
330C ILE 3.4 2.8 - - - +
331C ASN* 2.7 36.1 + - - +
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Residues in contact with GLY 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B VAL* 4.1 2.8 + - - +
91B ASP* 1.3 73.2 - - - +
93B SER* 1.3 62.7 + - - -
116B GLY 3.3 6.3 - - - -
117B VAL* 4.5 10.8 - - - -
329C SER* 3.3 6.5 - - - -
330C ILE* 2.7 45.2 + - - +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP* 5.2 5.2 + - - +
92B GLY* 1.3 74.8 + - - -
94B GLY* 1.3 59.7 + - - +
95B THR* 5.6 1.6 - - - -
114B GLN 4.6 0.4 - - - -
115B TYR* 3.5 10.1 - - - +
116B GLY* 2.7 39.6 + - - +
313B LEU* 5.5 1.0 - - - +
328C PRO* 3.8 5.8 - - - -
329C SER* 4.4 8.3 + - - -
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Residues in contact with GLY 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B SER* 1.3 77.3 - - - +
95B THR* 1.3 69.2 + - - -
114B GLN 3.5 7.0 - - - -
115B TYR* 3.7 14.1 - - - -
327C GLN* 3.3 23.2 - - - +
328C PRO* 3.1 26.3 + - - +
329C SER* 5.2 0.2 + - - -
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B SER* 5.6 1.7 - - - -
94B GLY* 1.3 81.0 + - - -
96B ARG* 1.3 61.9 + - - +
97B GLN* 4.6 15.9 - - + +
112B SER 3.6 0.9 - - - +
113B SER* 3.0 7.4 - - - -
114B GLN* 3.0 49.6 + - + +
115B TYR* 4.6 3.5 - - - -
325C LEU* 4.0 13.5 - - + -
326C PHE 3.4 4.5 + - - -
327C GLN* 3.5 27.1 + - - +
328C PRO* 4.7 0.2 - - - +
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Residues in contact with ARG 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR* 1.3 76.4 - - - +
97B GLN* 1.3 61.3 + - - +
111B ILE* 3.6 28.5 - - + +
112B SER 3.6 3.8 - - - +
113B SER* 3.8 14.1 + - - -
115B TYR* 3.2 30.0 + - + +
324C TRP* 3.6 22.0 + - - +
325C LEU* 3.4 2.5 - - - +
326C PHE* 2.8 56.0 + - + +
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR* 4.6 17.0 - - + +
96B ARG* 1.3 75.4 - - - +
98B ARG* 1.3 64.3 + - - +
99B LEU* 3.7 30.4 + - + +
110B ALA 3.7 0.7 - - - +
111B ILE* 3.4 7.4 - - - +
112B SER* 3.1 51.3 + - - +
324C TRP* 3.3 16.1 - - - +
325C LEU* 3.9 14.9 - - + +
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLN* 1.3 73.0 - - - +
99B LEU* 1.3 70.2 + - - +
109B PRO* 5.8 4.5 - - + -
110B ALA 3.4 12.1 - - - +
111B ILE* 4.5 8.1 - - + -
307C GLY 4.9 1.0 + - - -
322C GLY* 3.3 40.0 + - - +
323C SER* 3.3 29.9 + - - +
324C TRP* 3.1 64.6 + - + +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLN* 3.7 37.0 + - - +
98B ARG* 1.3 82.4 - - - +
100B PRO* 1.3 79.0 - - + +
103B LEU* 4.5 22.0 - - + +
104B SER* 4.4 15.9 - - - +
109B PRO* 3.4 2.8 - - - +
110B ALA* 3.0 31.4 + - + +
112B SER* 4.2 10.5 - - - +
114C GLN* 5.9 0.4 - - - +
309C MET* 4.7 20.9 - - + -
322C GLY 4.6 1.8 - - - -
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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