Contacts of the strand formed by residues 87 - 98 (chain C) in PDB entry 3IT8
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 TYR 87 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ALA* 3.1 18.7 + - + +
85C VAL 3.3 0.8 - - - -
86C SER* 1.3 80.1 - - - +
88C GLN* 1.3 53.7 + - - +
89C THR* 2.6 44.6 + - - +
91C VAL* 4.3 4.3 - - + -
58E HIS* 2.6 40.3 + + - +
153E ALA 5.5 0.9 - - - -
157E GLY* 3.4 28.7 - - - +
158E PHE* 4.7 2.0 - + - -
160E TYR* 4.3 12.8 - - + -
161E MET* 4.1 16.2 - - + -
162E GLY* 3.3 30.7 - - - -
165E LEU* 4.0 11.0 - - + -
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Residues in contact with GLN 88 (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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83C ILE* 3.4 23.3 - - + -
84C ALA 3.2 5.6 + - - -
85C VAL* 3.0 32.8 + - - +
86C SER 4.4 0.4 - - - -
87C TYR* 1.3 65.0 - - - +
89C THR* 1.3 66.4 + - - +
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Residues in contact with THR 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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82C ARG 3.2 9.9 - - - +
83C ILE* 3.7 9.7 - - - +
84C ALA 4.6 0.2 + - - -
87C TYR* 2.6 38.5 + - - +
88C GLN* 1.3 81.3 + - - +
90C LYS* 1.3 79.3 + - + +
91C VAL* 3.1 9.9 + - - +
58E HIS* 4.4 15.7 - - + +
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Residues in contact with LYS 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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47C GLN* 3.9 17.8 - - - +
81C SER* 3.9 21.3 - - - +
82C ARG 3.6 5.6 - - - -
83C ILE* 4.2 12.0 - - + +
89C THR* 1.3 82.8 - - + +
91C VAL* 1.3 61.9 + - - +
92C ASN* 4.3 2.6 - - - +
133C SER* 4.0 9.0 - - - -
135C GLU* 3.1 39.9 + - - +
58E HIS* 5.0 2.9 - - - -
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASN* 3.8 24.5 - - - +
81C SER* 4.3 0.7 - - - -
82C ARG* 3.0 45.7 + - + +
84C ALA* 5.8 0.9 - - + +
87C TYR* 4.3 9.2 - - + -
89C THR 3.5 9.2 - - - +
90C LYS* 1.3 78.8 - - - +
92C ASN* 1.3 65.8 + - - +
93C LEU 3.5 0.3 + - - -
58E HIS* 4.5 5.4 - - + +
161E MET* 4.1 13.5 - - + -
165E LEU* 3.5 33.7 - - + -
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Residues in contact with ASN 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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34B ASN* 4.8 5.0 + - - +
146B GLU* 2.5 38.2 + - - +
147B SER* 4.1 14.7 + - - -
148B GLY 4.6 2.7 + - - +
79C THR* 3.6 19.5 + - - +
80C ILE 3.9 4.3 - - - +
81C SER* 3.2 18.2 + - - +
90C LYS* 5.2 2.4 - - - +
91C VAL* 1.3 74.3 + - - +
93C LEU* 1.3 64.6 + - - +
94C LEU 4.9 2.0 - - - +
95C SER* 4.7 5.9 + - - -
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Residues in contact with LEU 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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15B HIS* 4.8 2.8 + - - -
34B ASN* 3.5 44.2 - - + +
148B GLY* 3.5 14.9 - - - -
151B TYR* 5.0 0.3 - - - -
58C ILE* 3.9 27.8 - - + -
80C ILE* 2.9 16.7 + - + +
81C SER 4.7 1.3 - - - -
82C ARG* 3.7 34.5 - - + +
91C VAL 4.2 1.3 - - - +
92C ASN* 1.3 76.5 - - - +
94C LEU* 1.3 73.7 + - + +
124C PHE* 3.6 33.9 - - + -
126C LEU* 5.0 0.2 - - + -
132C LEU* 4.1 6.5 - - + -
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Residues in contact with LEU 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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148B GLY* 3.4 5.2 - - - +
151B TYR* 3.4 37.2 - - + +
58C ILE* 3.9 6.7 - - + +
79C THR* 3.2 1.6 + - - -
80C ILE* 2.8 53.8 + - + +
92C ASN* 5.0 0.7 - - - +
93C LEU* 1.3 88.6 + - + +
95C SER* 1.3 63.6 + - - +
120C LEU* 3.7 17.5 - - + -
121C GLY* 3.6 32.3 - - - +
122C GLY* 3.7 3.8 - - - +
124C PHE* 3.6 25.6 - - + -
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Residues in contact with SER 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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61B GLN* 3.4 6.1 - - - +
63B LEU* 5.0 0.2 - - - +
146B GLU* 3.7 31.6 + - - +
148B GLY 2.7 19.0 + - - +
149B GLN* 3.2 22.8 + - - +
77C THR* 5.5 1.4 - - - -
78C HIS 3.4 10.2 + - - -
79C THR* 3.7 16.5 - - - +
92C ASN* 4.7 3.2 + - - -
94C LEU* 1.3 79.9 - - - +
96C ALA* 1.3 66.9 + - - +
97C ILE* 5.1 1.9 - - - +
120C LEU* 4.0 6.2 - - - +
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Residues in contact with ALA 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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61B GLN* 4.1 5.2 - - - +
63B LEU* 4.6 5.8 - - + -
117B PRO* 4.1 21.1 - - + -
77C THR* 3.4 4.7 - - - -
78C HIS 3.0 31.0 + - - +
95C SER* 1.3 77.4 + - - +
97C ILE* 1.3 67.6 + - - +
118C ILE* 3.8 20.1 - - + +
120C LEU* 3.7 18.6 - - + +
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Residues in contact with ILE 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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63B LEU* 4.1 9.4 - - + +
115B TYR* 3.5 56.9 - - + +
117B PRO* 3.4 21.0 - - - +
143B LEU* 4.4 1.6 - - + -
149B GLN* 3.5 27.6 - - - +
75C LEU* 4.4 15.9 - - + -
76C LEU 3.3 11.2 - - - +
77C THR* 4.2 17.3 - - + -
95C SER* 5.1 2.5 - - - +
96C ALA* 1.3 81.8 - - - +
98C LYS* 1.3 65.2 + - - +
118C ILE* 4.7 1.1 - - - -
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Residues in contact with LYS 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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98A LYS* 3.5 14.8 - - - +
98B LYS* 3.5 28.3 - - - +
115B TYR* 4.0 9.4 - - - +
116B GLU* 3.7 9.2 - - - +
117B PRO* 4.1 13.6 - - + +
75C LEU* 3.9 1.1 - - - -
76C LEU* 2.8 36.8 + - + +
97C ILE* 1.3 77.8 - - - +
99C SER* 1.3 62.8 - - - +
100C PRO* 3.3 5.9 - - - +
116C GLU* 3.1 46.3 + - + +
117C PRO* 2.8 28.3 + - - +
118C ILE* 4.0 19.7 - - + -
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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