Contacts of the strand formed by residues 87 - 98 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I ALA* 3.1 21.5 + - + +
85I VAL 3.3 0.8 - - - -
86I SER* 1.3 79.9 - - - +
88I GLN* 1.3 55.1 + - - +
89I THR* 2.6 40.0 + - - +
91I VAL* 4.3 4.7 - - + -
57J PRO 5.1 0.2 + - - -
58J HIS* 2.5 53.5 + + - +
153J ALA 5.6 0.9 - - - -
157J GLY* 3.8 24.9 - - - +
158J PHE* 5.0 2.2 - + - -
160J TYR* 4.7 8.3 - - + -
161J MET* 4.3 15.5 - - + -
162J GLY* 3.5 27.5 - - - -
165J LEU* 4.0 7.0 - - + -
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Residues in contact with GLN 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I ILE* 3.4 24.0 - - + -
84I ALA 3.2 5.6 + - - -
85I VAL* 3.0 32.6 + - - +
86I SER 4.4 0.6 - - - -
87I TYR* 1.3 65.3 - - - +
89I THR* 1.3 66.4 + - - +
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Residues in contact with THR 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I ARG 3.1 10.4 - - - +
83I ILE* 3.7 9.7 - - - +
84I ALA 4.6 0.2 + - - -
87I TYR* 2.6 38.3 + - - +
88I GLN* 1.3 77.1 + - - +
90I LYS* 1.3 77.6 + - + +
91I VAL* 3.1 10.0 + - - +
58J HIS* 4.3 15.9 - - + +
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Residues in contact with LYS 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I GLN* 3.9 16.6 - - - +
81I SER* 3.8 20.9 - - - +
82I ARG 3.6 5.4 - - - -
83I ILE* 4.2 12.5 - - + +
89I THR* 1.3 83.4 - - + +
91I VAL* 1.3 61.9 + - - +
92I ASN* 4.2 3.0 - - - +
133I SER* 4.0 8.7 - - - -
135I GLU* 3.1 40.5 + - - +
58J HIS* 4.9 2.9 + - - -
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Residues in contact with VAL 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ASN* 3.8 24.2 - - - +
81I SER* 3.5 0.8 - - - -
82I ARG* 3.0 48.8 + - + +
84I ALA* 5.8 1.1 - - + +
87I TYR* 4.3 8.3 - - + -
89I THR 3.6 8.5 - - - +
90I LYS* 1.3 79.3 - - - +
92I ASN* 1.3 65.6 + - - +
93I LEU* 3.5 0.6 + - + +
58J HIS* 4.3 10.8 - - + +
161J MET* 4.2 10.1 - - - -
165J LEU* 3.6 33.2 - - + -
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Residues in contact with ASN 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ASN* 4.8 5.0 + - - +
146G GLU* 2.6 37.6 + - - +
147G SER* 4.3 13.6 + - - -
148G GLY* 4.7 3.5 + - - +
79I THR* 3.6 19.9 + - - +
80I ILE 3.8 3.8 - - - +
81I SER* 3.1 18.4 + - - +
90I LYS* 5.2 2.3 - - - +
91I VAL* 1.3 73.3 + - - +
93I LEU* 1.3 63.7 + - - +
94I LEU 4.8 2.5 - - - +
95I SER* 4.7 5.7 + - - -
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Residues in contact with LEU 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G HIS* 4.8 3.5 + - - -
34G ASN* 3.5 43.3 - - + +
148G GLY* 3.5 14.8 - - - -
151G TYR* 5.0 0.3 - - - -
58I ILE* 4.0 26.9 - - + -
80I ILE* 2.9 17.0 + - + +
81I SER 4.7 1.1 - - - -
82I ARG* 3.7 35.4 - - + +
91I VAL 4.2 1.6 - - - +
92I ASN* 1.3 77.0 - - - +
94I LEU* 1.3 73.9 + - + +
124I PHE* 3.6 33.9 - - + -
126I LEU* 5.1 0.2 - - + -
132I LEU* 4.1 7.0 - - + -
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Residues in contact with LEU 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G GLY* 3.5 4.7 - - - +
151G TYR* 3.4 39.0 - - + +
58I ILE* 4.0 6.7 - - + +
79I THR* 3.2 1.6 + - - -
80I ILE* 2.8 53.5 + - + +
92I ASN* 4.9 0.2 - - - +
93I LEU* 1.3 89.7 + - + +
95I SER* 1.3 64.2 + - - +
120I LEU* 3.6 16.4 - - + -
121I GLY* 3.6 31.6 - - - +
122I GLY* 3.7 3.8 - - - +
124I PHE* 3.7 24.7 - - + -
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Residues in contact with SER 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G GLN* 3.3 6.8 - - - +
146G GLU* 3.8 29.4 + - - +
148G GLY* 2.7 20.5 + - - +
149G GLN* 3.3 21.8 + - - +
77I THR* 5.5 1.2 - - - -
78I HIS 3.3 10.6 + - - -
79I THR* 3.6 16.7 - - - +
92I ASN* 4.7 4.0 + - - -
94I LEU* 1.3 77.5 - - - +
96I ALA* 1.3 66.8 + - - +
97I ILE* 5.1 2.1 - - - +
120I LEU* 4.0 6.2 - - - +
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Residues in contact with ALA 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G GLN* 4.0 9.9 - - - +
63G LEU* 4.6 5.4 - - + -
117G PRO* 4.1 16.2 - - + -
76I LEU 4.0 0.2 - - - +
77I THR* 3.4 4.7 - - - -
78I HIS 3.0 30.1 + - - +
95I SER* 1.3 78.4 + - - +
97I ILE* 1.3 68.1 + - - +
118I ILE* 3.8 19.2 - - + +
120I LEU* 3.7 19.3 - - + +
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Residues in contact with ILE 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G LEU* 4.0 8.6 - - + +
115G TYR* 3.5 55.8 - - + +
117G PRO* 3.4 20.8 - - - +
143G LEU* 4.5 1.8 - - + -
149G GLN* 3.4 28.0 - - - +
75I LEU* 4.4 16.8 - - + -
76I LEU 3.3 11.0 - - - +
77I THR* 4.2 18.8 - - + -
95I SER* 5.1 2.5 - - - +
96I ALA* 1.3 80.5 - - - +
98I LYS* 1.3 64.0 + - - +
118I ILE* 4.7 1.3 - - - -
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Residues in contact with LYS 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G LYS* 3.4 29.4 - - - +
115G TYR* 3.9 9.6 - - - +
116G GLU* 3.6 7.9 - - - +
117G PRO* 4.1 15.0 - - + +
98H LYS* 3.6 13.9 - - - +
75I LEU* 3.9 0.7 - - - -
76I LEU* 2.8 37.0 + - + +
97I ILE* 1.3 77.0 - - - +
99I SER* 1.3 63.6 + - - +
100I PRO* 3.3 5.9 - - - +
116I GLU* 3.1 45.4 + - + +
117I PRO* 2.9 28.9 + - - +
118I ILE* 3.9 20.4 - - + -
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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