Contacts of the strand formed by residues 111 - 118 (chain B) in PDB entry 5I74
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 ALA 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B LYS* 4.3 16.6 - - + -
58B GLN 3.2 16.8 - - - +
59B SER* 3.6 19.1 - - - +
60B HIS* 4.9 3.8 - - - +
109B ASP 3.3 7.3 + - - +
110B SER* 1.3 75.9 - - - +
112B VAL* 1.3 66.3 + - - +
113B TYR* 3.6 9.6 - - + -
132B THR 3.5 2.1 - - - +
133B THR* 5.5 0.9 - - - -
134B LEU 3.0 29.2 + - - -
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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
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58B GLN* 2.9 41.3 + - + +
59B SER 6.3 0.2 - - - -
60B HIS* 6.2 2.2 - - - +
111B ALA* 1.3 74.5 - - - +
113B TYR* 1.3 62.4 - - - +
114B TYR* 3.5 35.5 - - + +
130B GLN 5.5 0.2 - - - +
131B GLY* 4.3 2.2 - - - -
132B THR 3.3 19.7 - - - +
133B THR* 4.1 20.0 - - + +
173B GLU* 6.2 0.4 - - - +
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Residues in contact with TYR 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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25B GLN* 3.1 5.6 + - - -
39B ILE* 4.3 13.7 - - + -
55B TRP* 4.7 2.2 - - + -
56B VAL 3.6 2.2 - - - -
57B LYS* 3.5 43.5 - - + +
67B ILE* 4.0 10.5 - - + -
83B PHE* 5.9 0.7 - + - -
100B MET* 3.9 27.1 - - + -
102B LEU* 4.0 18.6 - - + +
109B ASP* 2.8 43.1 + - - +
111B ALA* 3.6 16.8 - - + -
112B VAL* 1.3 73.5 - - - +
114B TYR* 1.3 61.9 + - - +
131B GLY* 3.2 3.5 - - - -
132B THR* 2.7 42.9 + - - +
134B LEU* 3.6 19.3 - - + -
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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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25B GLN* 3.3 4.7 - - - -
55B TRP* 3.0 14.9 - - - -
56B VAL* 2.9 39.2 + - + +
58B GLN* 3.3 24.4 + - + -
64B LEU* 5.0 0.9 - - + -
112B VAL* 3.5 29.3 - - + +
113B TYR* 1.3 74.9 - - - +
115B CYS* 1.3 60.9 + - - +
116B THR 4.2 0.2 - - - -
128B TRP* 3.5 32.5 - + + -
129B GLY 3.3 19.5 - - - +
130B GLN 3.9 3.2 + - - -
131B GLY* 3.5 19.3 - - - -
58C GLN* 3.4 17.2 + - - -
62C GLN 3.7 6.9 + - - -
63C SER* 3.5 24.9 - - - -
64C PRO* 4.0 8.7 - - + -
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Residues in contact with CYS 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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23B LEU* 3.3 5.6 - - - +
25B GLN* 3.1 32.1 + - - -
41B CYS* 2.0 48.7 - - + -
53B MET* 4.3 3.4 - - - -
54B ASN 3.0 10.8 - - - +
55B TRP* 3.6 23.1 - - + -
114B TYR* 1.3 73.1 - - - +
116B THR* 1.3 61.2 + - - +
129B GLY* 2.8 29.0 + - - -
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Residues in contact with THR 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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23B LEU* 3.8 2.5 - - - -
53B MET* 3.8 3.0 - - - +
54B ASN* 2.9 47.1 + - + +
56B VAL* 4.1 15.0 - - + -
115B CYS* 1.3 76.1 - - - +
117B ARG* 1.3 60.1 + - - +
125B PHE* 3.1 45.2 - - + +
127B TYR 2.7 22.8 + - - -
128B TRP* 3.6 18.3 - - + -
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Residues in contact with ARG 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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701A NAG 6.3 1.0 - - - +
21B VAL* 4.4 3.2 - - - +
23B LEU* 3.6 12.0 - - + +
46B TYR* 3.4 64.1 - - + +
51B TYR* 3.5 50.0 + - + -
52B TYR 3.6 4.9 - - - +
53B MET* 4.7 2.7 - - + -
116B THR* 1.3 72.3 + - - +
118B SER* 1.3 62.5 + - - +
125B PHE* 3.4 7.6 - - - -
126B ASP* 2.6 62.1 + - - +
127B TYR* 2.9 35.9 + - + +
75C TYR* 4.3 3.6 + - - -
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Residues in contact with SER 118 (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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51B TYR* 3.4 8.8 - - - +
52B TYR* 2.9 34.2 + - - +
54B ASN* 2.4 32.2 + - - -
117B ARG* 1.3 74.7 - - - +
119B PRO* 1.3 66.9 - - - +
123B TYR* 3.3 23.3 + - - -
124B TYR 3.2 14.4 - - - -
125B PHE* 3.7 10.8 - - - -
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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