Contacts of the strand formed by residues 91 - 101 (chain I) in PDB entry 5C3I
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 GLY 91 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88I ASP 4.2 4.5 - - - +
89I ALA 3.6 0.7 + - - +
90I VAL* 1.3 76.0 - - - +
92I VAL* 1.3 64.6 + - - -
93I THR 3.6 0.5 + - - -
113I VAL 3.4 2.9 - - - +
114I ASN* 3.8 11.4 - - - -
115I ASN* 2.8 39.7 + - - -
114J ALA* 5.3 7.6 - - - -
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Residues in contact with VAL 92 (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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88I ASP* 4.7 5.4 - - - +
91I GLY* 1.3 71.5 - - - -
93I THR* 1.3 64.9 + - - +
112I TYR* 3.8 32.5 - - + -
113I VAL 3.3 5.6 - - - +
114I ASN* 3.5 26.9 - - + +
140I LEU* 5.4 4.0 - - + -
109J LEU 5.2 0.2 - - - +
110J CYS* 3.9 38.8 - - + +
113J HIS* 4.2 7.0 - - + -
114J ALA* 4.0 16.3 - - + +
116J ARG* 6.2 0.4 - - - +
122J LYS* 5.1 7.1 + - - -
126J LEU* 3.9 11.7 - - + +
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Residues in contact with THR 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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44I TYR* 3.3 32.2 - - + +
45I VAL* 2.6 29.8 + - - +
46I GLY 4.7 3.6 + - - -
88I ASP* 4.8 11.0 - - - +
91I GLY 4.4 0.7 - - - +
92I VAL* 1.3 76.2 - - - +
94I VAL* 1.3 65.0 + - - +
112I TYR* 3.3 7.4 - - - -
113I VAL* 2.5 51.0 + - + +
115I ASN* 3.6 10.5 - - - +
126J LEU* 4.5 9.1 - - - +
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Residues in contact with VAL 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I TYR* 3.8 4.3 - - - -
45I VAL* 3.0 54.7 + - + -
93I THR* 1.3 90.8 + - - +
95I VAL* 1.3 65.3 + - - +
96I LEU* 4.4 12.6 - - + -
111I TYR 3.3 6.7 - - - +
112I TYR* 3.5 30.5 - - + -
113I VAL* 4.2 1.3 - - - -
126J LEU* 3.8 17.8 - - + +
129J ARG* 5.3 1.3 - - + -
130J ILE* 3.7 26.5 - - + +
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Residues in contact with VAL 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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22I PHE* 3.6 25.1 - - + -
24I PHE* 4.3 19.3 - - + -
42I ILE* 4.1 17.0 - - + -
43I ILE 3.3 10.3 - - - +
44I TYR* 3.6 22.0 - - + -
57I LEU* 5.3 0.2 - - + -
94I VAL* 1.3 72.7 - - - +
96I LEU* 1.3 75.0 + - - +
97I ILE* 5.2 0.4 - - + -
109I VAL 4.1 0.3 - - - +
110I GLY* 3.4 2.3 - - - -
111I TYR* 2.8 39.9 + - + +
113I VAL* 3.4 22.4 - - + +
139I ILE* 5.4 1.1 - - + -
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Residues in contact with LEU 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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41I LYS 3.6 0.3 - - - +
42I ILE* 3.4 4.9 - - - -
43I ILE* 2.7 53.2 + - + +
45I VAL* 4.2 19.1 - - + -
94I VAL* 4.4 9.6 - - + -
95I VAL* 1.3 79.2 - - - +
97I ILE* 1.3 64.4 + - - +
98I THR* 4.0 12.6 - - + -
108I ARG* 3.5 36.6 - - + +
109I VAL 3.6 2.5 - - - +
110I GLY* 3.9 19.7 - - - -
129J ARG* 4.7 8.7 - - - +
130J ILE* 3.9 26.5 - - + -
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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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9I VAL* 4.0 17.7 - - + -
24I PHE* 3.6 56.3 - - + -
26I ILE* 4.3 12.8 - - + -
40I TRP* 4.1 26.0 - - + -
41I LYS 3.4 8.3 - - - +
42I ILE* 4.6 9.9 - - + -
74I PHE* 5.3 1.3 - - + -
95I VAL* 5.2 0.2 - - + -
96I LEU* 1.3 76.8 - - - +
98I THR* 1.3 60.8 + - - +
99I CYS 4.4 0.2 + - - -
107I ILE* 4.2 1.7 - - - +
108I ARG* 3.6 0.9 - - - -
109I VAL* 2.7 49.3 + - + +
111I TYR* 4.2 10.8 - - + -
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Residues in contact with THR 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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39I GLU 3.6 0.9 - - - +
40I TRP* 3.3 5.8 - - - +
41I LYS* 2.7 62.3 + - - +
43I ILE* 4.1 8.2 - - + +
96I LEU* 4.2 11.4 - - + -
97I ILE* 1.3 78.4 - - - +
99I CYS* 1.3 59.5 + - - +
100I THR* 5.2 3.3 - - - +
105I GLU* 3.4 35.6 + - - +
107I ILE 3.6 4.0 - - - -
108I ARG* 3.5 25.4 - - + +
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Residues in contact with CYS 99 (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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38I LEU* 3.9 18.4 - - - -
39I GLU 3.2 9.4 - - - -
40I TRP* 3.6 44.9 - - + -
98I THR* 1.3 74.7 - - - +
100I THR* 1.3 65.8 + - - +
105I GLU* 3.4 4.7 - - - +
106I PHE* 3.2 53.0 + - + -
107I ILE* 3.1 15.2 + - + +
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Residues in contact with THR 100 (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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37I ASP 4.0 1.0 - - - +
38I LEU* 3.7 6.4 - - - -
39I GLU* 2.9 56.7 + - - +
41I LYS* 5.6 8.4 - - + +
98I THR* 5.2 4.5 - - - +
99I CYS* 1.3 77.0 - - - +
101I TYR* 1.3 59.9 + - - +
103I GLY* 4.1 10.7 - - - +
104I GLN 3.2 15.3 - - - +
105I GLU* 3.5 32.8 - - + +
106I PHE* 3.9 2.9 - - - -
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Residues in contact with TYR 101 (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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3I LYS* 4.0 4.3 + - - -
34I LEU* 3.5 30.4 - - + +
35I SER* 2.9 27.2 + - - -
36I GLU* 3.1 43.3 + - + +
37I ASP 3.8 11.9 - - - -
38I LEU* 3.8 13.7 - - + -
100I THR* 1.3 73.0 - - - +
102I ARG* 1.3 74.1 + - + +
104I GLN* 2.8 27.5 + - - +
106I PHE* 3.9 9.7 - - + -
151I ILE* 4.2 3.5 - - + +
152I ASN 4.7 3.0 - - - +
153I TRP* 3.7 58.7 + + + -
154I GLU* 5.4 1.1 - - - -
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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