Contacts of the strand formed by residues 72 - 81 (chain B) in PDB entry 4BEI
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 VAL 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 5.6 7.4 - - + -
40B ILE* 3.8 28.3 - - + -
66B ASN* 3.4 35.6 - - + +
68B SER* 5.4 2.7 - - - -
70B GLU 4.9 0.7 - - - +
71B THR* 1.3 74.1 + - - +
73B LYS* 1.3 72.4 + - - +
74B PHE* 3.9 6.0 - - + -
105B ALA* 3.3 4.9 - - - +
106B LEU* 2.9 40.8 + - + +
137B ALA* 4.7 10.3 - - + -
138B GLU* 5.3 3.1 - - + +
139B ASN* 6.3 1.8 - - - +
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Residues in contact with LYS 73 (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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71B THR 4.4 0.6 + - - -
72B VAL* 1.3 80.1 - - - +
74B PHE* 1.3 63.0 + - - +
103B SER* 5.3 6.5 - - - +
104B ASP 3.3 9.9 - - - +
105B ALA* 4.3 5.6 - - + +
138B GLU* 2.9 52.9 + - + +
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Residues in contact with PHE 74 (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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40B ILE* 4.0 14.1 - - + -
64B ILE* 3.9 24.7 - - + -
72B VAL* 3.9 6.7 - - + -
73B LYS* 1.3 79.2 - - - +
75B LYS* 1.3 67.6 + - - +
76B TYR* 3.7 24.5 - + + -
103B SER* 4.3 4.1 + - - -
104B ASP* 2.7 53.6 + - + +
105B ALA* 4.0 11.9 - - - -
106B LEU* 3.8 32.1 - - + -
112B LEU* 4.3 8.7 - - + -
135B VAL* 3.8 22.9 - - + -
136B VAL 3.4 12.8 - - - +
137B ALA* 3.8 10.1 - - + +
138B GLU* 4.2 1.8 - - - +
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Residues in contact with LYS 75 (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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237A ASN* 5.5 3.7 - - - +
239A ASP* 2.9 40.4 + - - -
241A SER* 4.9 3.1 - - - +
242A TYR* 3.9 25.8 - - + +
74B PHE* 1.3 74.5 - - - +
76B TYR* 1.3 62.9 + - - +
77B TRP* 4.0 14.3 - - + -
101B GLN* 2.8 30.9 + - + +
102B GLU 3.9 12.1 - - - +
103B SER* 3.4 30.9 + - - +
135B VAL* 3.5 1.4 - - - +
136B VAL* 2.7 43.6 + - + +
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Residues in contact with TYR 76 (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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62B LEU* 3.9 21.5 - - + -
64B ILE* 3.7 24.2 - - + -
74B PHE* 3.7 18.4 - + + -
75B LYS* 1.3 77.9 - - - +
77B TRP* 1.3 74.7 - - - +
101B GLN* 3.3 14.6 + - - -
102B GLU 4.8 2.8 + - - +
104B ASP* 3.7 23.1 + - + -
112B LEU* 4.0 16.3 - - + +
114B VAL* 3.7 23.2 - - + +
116B ARG* 4.0 19.1 + - - -
133B LEU* 3.9 9.9 - - + -
134B GLN 3.2 14.4 - - - +
135B VAL* 4.1 5.6 - - + -
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Residues in contact with TRP 77 (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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212A LEU* 4.2 8.3 - - + -
213A ILE 3.2 10.7 + - - -
214A ILE* 3.5 28.0 - - + -
215A PRO* 3.4 30.7 - - + -
242A TYR* 3.6 33.9 - + - -
75B LYS* 4.0 13.9 - - + -
76B TYR* 1.3 95.7 - - - +
78B LEU* 1.3 60.4 + - - +
79B SER* 3.6 6.1 - - - -
101B GLN* 3.6 27.4 - - + +
116B ARG* 4.5 7.4 - - - +
132B SER 3.8 0.2 - - - +
133B LEU* 3.8 4.5 - - - +
134B GLN* 3.0 57.8 + - + +
136B VAL* 3.6 29.2 - - + -
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Residues in contact with LEU 78 (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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215A PRO* 4.5 3.0 - - - +
44B LEU* 4.2 2.9 - - + -
60B SER* 3.8 20.0 - - - +
62B LEU* 4.1 19.5 - - + -
77B TRP* 1.3 76.8 - - - +
79B SER* 1.3 62.8 + - - +
89B PRO* 3.9 3.1 - - - +
90B ALA* 2.9 40.4 + - + +
91B LYS* 4.4 1.7 + - - +
116B ARG* 3.8 33.3 + - + +
117B GLY 6.1 0.2 - - - +
118B PHE* 4.4 14.1 - - + -
131B VAL* 3.8 15.9 - - + -
132B SER 3.6 15.7 - - - +
133B LEU* 3.7 21.8 - - + +
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Residues in contact with SER 79 (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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205A THR* 5.7 0.3 - - - +
213A ILE* 2.6 50.6 + - - +
215A PRO* 3.6 8.7 - - - +
77B TRP* 3.6 9.0 - - - -
78B LEU* 1.3 76.1 + - - +
80B ILE* 1.3 64.0 + - - +
88B PHE 3.8 6.5 - - - -
89B PRO* 4.6 1.7 - - - +
90B ALA 4.2 0.2 - - - +
130B THR 3.9 0.2 - - - +
131B VAL* 3.6 1.4 - - - -
132B SER* 2.8 44.3 + - - +
134B GLN* 4.9 3.1 - - - -
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Residues in contact with ILE 80 (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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213A ILE* 4.6 6.1 - - - +
79B SER* 1.3 83.4 - - - +
81B LYS* 1.3 63.3 + - - +
82B GLY 4.3 0.2 - - - -
87B TYR* 3.5 4.7 - - - +
88B PHE* 2.8 83.7 + - + +
90B ALA* 4.2 14.6 - - + -
118B PHE* 3.8 17.5 - - + -
129B TYR* 3.8 18.8 - - + -
130B THR 3.4 7.6 - - - +
131B VAL* 3.6 30.1 - - + -
149B PHE* 4.2 10.3 - - + -
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Residues in contact with LYS 81 (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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213A ILE* 3.9 14.1 - - + -
80B ILE* 1.3 75.5 - - - +
82B GLY* 1.3 64.1 + - - +
86B ILE 3.5 9.9 - - - +
87B TYR* 3.6 23.6 - - + -
128B LYS 4.4 0.5 - - - +
129B TYR* 3.4 4.0 - - - -
130B THR* 2.7 49.6 + - - +
248B THR* 4.2 1.2 - - - +
1272B O4B 2.7 110.0 + - - +
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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