Contacts of the strand formed by residues 88 - 99 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A PRO* 4.0 1.8 - - - +
334A ILE* 2.9 8.3 + - + -
335A PHE* 2.8 66.6 + - + +
86C PRO* 3.3 23.5 + - + +
87C ARG* 1.3 75.4 - - - +
89C GLY* 1.3 61.4 + - - +
119C LEU* 4.3 21.1 - - + -
120C GLY* 3.3 17.7 - - - +
121C THR* 4.6 4.0 - - - -
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Residues in contact with GLY 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ASN* 5.1 4.7 - - - -
332A LEU 3.2 14.1 - - - -
333A PRO* 4.2 2.9 - - - -
334A ILE* 3.8 6.1 - - - -
87C ARG 4.0 1.2 + - - -
88C ILE* 1.3 76.6 - - - +
90C VAL* 1.3 66.5 + - - -
91C ASP* 3.8 6.5 - - - +
119C LEU* 3.6 5.6 - - - +
120C GLY 3.0 31.0 + - - +
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Residues in contact with VAL 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ILE 3.7 1.0 - - - +
331A ASN* 3.4 5.9 + - - -
332A LEU* 2.8 46.9 + - + +
334A ILE* 3.8 26.7 - - + -
89C GLY* 1.3 72.3 - - - -
91C ASP* 1.3 66.7 + - - +
92C GLY* 4.1 1.6 - - - +
117C VAL* 4.2 21.1 - - + -
118C THR 3.4 10.3 - - - +
119C LEU* 3.8 14.1 - - + -
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Residues in contact with ASP 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ILE 3.5 3.3 - - - +
331A ASN* 2.6 33.3 + - - +
89C GLY 3.8 10.3 - - - +
90C VAL* 1.3 74.3 - - - +
92C GLY* 1.3 61.4 + - - +
93C SER* 3.9 3.4 + - - -
116C GLY 3.5 2.8 - - - +
117C VAL* 3.5 2.8 - - - -
118C THR* 2.7 57.5 + - + +
120C GLY 4.6 8.3 + - - +
121C THR 5.8 0.2 - - - -
122C THR* 4.7 11.4 + - - -
305C ASN* 5.5 1.0 + - - +
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Residues in contact with GLY 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A SER* 3.3 6.6 - - - -
330A ILE* 2.8 54.0 + - - +
90C VAL* 4.1 3.0 - - - +
91C ASP* 1.3 73.2 - - - +
93C SER* 1.3 59.0 + - - -
116C GLY 3.4 5.8 - - - -
117C VAL* 4.5 8.5 - - - -
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Residues in contact with SER 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A GLN* 5.5 2.6 - - - +
328A PRO 3.8 4.6 + - - -
329A SER* 4.8 5.2 + - - +
330A ILE* 6.4 0.2 - - - -
91C ASP* 3.9 4.2 + - - -
92C GLY* 1.3 74.6 - - - -
94C GLY* 1.3 61.8 + - - +
95C THR* 4.3 8.8 + - - -
114C GLN 4.8 0.2 - - - -
115C TYR* 3.3 9.3 - - - +
116C GLY* 2.7 42.1 + - - +
313C LEU* 5.9 0.2 - - - +
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Residues in contact with GLY 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A GLN* 3.2 26.3 - - - +
328A PRO* 3.0 29.4 + - - +
93C SER* 1.3 76.0 + - - +
95C THR* 1.3 65.0 + - - -
114C GLN 3.7 4.7 - - - -
115C TYR* 4.0 13.9 - - - -
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Residues in contact with THR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A LEU* 4.1 15.0 - - + -
326A PHE 3.6 3.4 - - - -
327A GLN* 3.6 27.6 + - - +
93C SER* 4.3 6.9 + - - -
94C GLY* 1.3 79.3 + - - -
96C ARG* 1.3 66.3 + - - +
97C GLN* 4.8 14.4 - - + +
112C SER 5.1 1.3 - - - +
113C SER* 3.1 4.4 - - - -
114C GLN* 2.8 60.0 + - + +
115C TYR* 4.8 4.8 - - - -
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Residues in contact with ARG 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A TRP* 3.9 15.9 + - - +
326A PHE* 3.1 41.8 + - + +
95C THR* 1.3 76.6 - - - +
97C GLN* 1.3 59.3 + - - +
111C ILE* 3.8 35.5 - - + +
112C SER 3.7 3.4 - - - -
113C SER* 3.6 20.4 - - - -
115C TYR* 5.0 10.8 - - + +
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Residues in contact with GLN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A MET* 5.7 1.9 - - - +
324A TRP* 3.3 19.7 - - - +
325A LEU* 3.9 22.9 - - + +
95C THR* 4.8 10.6 - - + +
96C ARG* 1.3 75.8 - - - +
98C ARG* 1.3 60.0 + - - +
99C LEU* 3.7 32.2 + - + +
110C ALA 3.7 1.0 - - - +
111C ILE* 3.4 4.3 - - - -
112C SER* 3.1 47.3 + - - +
114C GLN* 6.1 1.2 - - - +
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Residues in contact with ARG 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A GLY 5.0 9.2 - - - +
323A SER* 3.4 25.2 - - - -
324A TRP* 3.4 60.4 + - + +
97C GLN* 1.3 72.0 - - - +
99C LEU* 1.3 70.4 + - - +
109C PRO* 4.5 26.4 + - + +
110C ALA* 3.5 12.3 - - - +
111C ILE* 3.3 32.4 - - + +
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLN* 4.5 7.9 - - - +
309A MET* 4.0 22.2 - - + -
322A GLY 4.8 1.8 - - - -
97C GLN* 3.7 35.9 + - + +
98C ARG* 1.3 81.4 - - - +
100C PRO* 1.3 74.0 - - + +
103C LEU* 4.0 30.3 - - + -
104C SER* 4.2 12.8 + - - +
109C PRO* 3.3 2.4 - - - +
110C ALA 3.0 31.0 + - - +
112C SER* 4.1 12.8 - - - +
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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