Contacts of the strand formed by residues 108 - 117 (chain B) in PDB entry 5I0X
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 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ASN* 3.6 10.5 - - - -
78B ASP* 3.6 15.3 - - - -
106B GLY 3.6 2.0 + - - -
107B VAL* 1.3 80.0 - - - +
109B ASN* 1.3 61.8 + - - -
110B TYR* 3.3 9.0 - - - -
148B LYS* 3.6 8.2 - - - +
149B TYR 2.9 33.6 + - - -
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Residues in contact with ASN 109 (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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77B ASN* 2.7 42.6 + - + +
78B ASP* 3.0 26.7 + - - +
108B GLY* 1.3 71.2 - - - -
110B TYR* 1.3 57.0 + - - +
147B PHE 3.8 4.2 - - - +
148B LYS* 3.5 29.3 - - - +
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Residues in contact with TYR 110 (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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74B LEU* 3.5 20.9 - - + -
75B VAL 3.2 16.8 - - - -
76B ASN* 3.7 23.6 - - + -
77B ASN* 4.3 2.7 - - - -
104B MET* 3.7 15.9 - - + +
105B MET* 2.9 42.0 + - + -
106B GLY 2.7 29.9 + - - -
108B GLY 3.3 16.2 - - - -
109B ASN* 1.3 75.2 - - - +
111B LYS* 1.3 59.5 + - - +
112B VAL 4.3 0.2 - - - -
146B GLU* 3.3 6.6 - - - +
147B PHE* 2.8 56.4 + + + +
149B TYR* 3.7 20.9 - + + -
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Residues in contact with LYS 111 (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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73B THR 3.8 1.4 - - - +
74B LEU* 3.7 2.1 - - - +
75B VAL* 2.9 40.0 + - + +
77B ASN* 3.9 17.1 + - - +
110B TYR* 1.3 75.7 - - - +
112B VAL* 1.3 65.0 + - - +
113B THR* 3.9 8.3 - - - +
144B SER* 3.4 33.6 - - - -
145B TYR 3.2 10.1 - - - +
146B GLU* 4.3 20.8 + - + +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 5.3 0.2 - - + -
21B ALA* 5.0 2.2 - - + -
45B LEU* 4.2 11.7 - - + -
72B TYR* 4.1 14.1 - - + -
73B THR 3.4 9.9 - - - +
74B LEU* 3.8 22.4 - - + -
110B TYR 4.3 0.2 - - - -
111B LYS* 1.3 74.9 - - - +
113B THR* 1.3 64.6 + - - +
114B TYR* 3.8 33.9 - - + +
144B SER* 3.2 2.9 - - - -
145B TYR* 2.8 51.7 + - + +
147B PHE* 4.0 17.2 - - + -
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Residues in contact with THR 113 (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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72B TYR* 3.1 7.6 - - - +
73B THR* 2.9 40.2 + - - +
111B LYS* 3.9 11.4 - - - +
112B VAL* 1.3 74.5 - - - +
114B TYR* 1.3 63.8 + - - +
115B HIS* 3.8 18.2 - - + -
142B ASP* 3.7 31.4 - - + +
143B VAL 3.3 7.6 - - - +
144B SER* 2.8 21.9 + - - +
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Residues in contact with TYR 114 (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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19B LEU* 6.1 0.9 - - + -
20B ALA 4.4 1.3 - - - -
21B ALA* 3.4 15.1 - - + +
45B LEU* 3.4 17.5 - - + +
46B GLU 2.7 21.7 + - - -
47B ALA* 3.5 30.7 - - + -
49B ILE* 5.6 1.1 - - + -
70B ILE* 4.1 13.0 - - + -
71B SER 3.4 3.4 - - - -
72B TYR* 4.0 8.3 - - + -
87B PHE* 3.5 23.6 - + - -
112B VAL* 3.8 24.6 - - + +
113B THR* 1.3 77.5 - - - +
115B HIS* 1.3 62.7 - - - +
116B ILE* 3.8 9.3 + - + +
141B PHE 3.8 0.7 - - - +
142B ASP* 3.2 4.7 - - - -
143B VAL* 2.8 45.0 + - + -
145B TYR* 3.7 25.6 - + - -
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Residues in contact with HIS 115 (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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69B THR 3.4 2.3 - - - +
70B ILE* 3.3 6.4 - - - -
71B SER* 2.8 57.3 + - - +
72B TYR 4.1 0.9 - - - -
73B THR* 2.8 32.2 + - - -
84B GLU* 4.7 1.3 + - - -
113B THR* 3.8 17.7 - - + +
114B TYR* 1.3 70.9 - - - +
116B ILE* 1.3 59.5 + - - +
117B GLU* 5.3 3.1 - - + +
142B ASP* 2.8 21.2 + - - -
201B CU 2.0 32.6 - - - -
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Residues in contact with ILE 116 (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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17B MET* 5.6 0.7 - - + -
19B LEU* 3.3 32.3 - - + -
49B ILE* 4.2 9.9 - - + -
68B LEU* 4.2 16.8 - - + -
69B THR 3.5 1.8 - - - -
70B ILE* 4.2 14.1 - - + -
114B TYR* 3.9 14.8 - - + +
115B HIS* 1.3 77.7 - - - +
117B GLU* 1.3 68.4 + - - +
138B TRP* 3.8 25.7 - - + -
140B PRO* 3.2 6.0 - - - +
141B PHE* 2.8 48.9 + - + +
143B VAL* 4.0 17.5 - - + -
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Residues in contact with GLU 117 (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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68B LEU* 3.5 10.2 - - - +
69B THR* 2.9 57.1 + - - +
71B SER* 5.3 3.8 + - - -
115B HIS 5.3 3.1 - - - +
116B ILE* 1.3 77.9 - - - +
118B PRO* 1.3 72.1 - - + +
121B LYS* 3.8 25.3 - - + +
138B TRP* 3.9 2.5 - - - -
140B PRO* 4.1 17.1 - - + +
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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