Contacts of the strand formed by residues 127 - 137 (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 GLY 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B PRO* 4.2 5.8 - - - -
125B ALA 3.7 1.4 + - - -
126B ASP* 1.3 75.0 - - - +
128B LYS* 1.3 62.8 + - - -
129B TYR* 3.5 7.5 - - - -
150B VAL* 3.4 2.9 - - - -
151B LYS* 2.8 34.4 + - - +
153B VAL* 4.3 18.6 - - - +
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Residues in contact with LYS 128 (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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81B LYS 4.4 0.2 - - - +
82B GLY* 3.9 2.4 - - - -
83B PRO* 3.5 22.8 - - - +
127B GLY* 1.3 72.5 - - - -
129B TYR* 1.3 68.2 + - - +
130B THR* 5.5 2.9 - - - +
148B GLU* 4.0 29.6 - - + +
149B PHE 3.9 7.9 - - - +
150B VAL* 4.3 13.0 - - + -
153B VAL* 4.9 0.8 - - + +
155B LEU* 6.5 0.2 - - + -
264B GLN* 5.8 5.8 - - - +
265B SER 6.1 0.4 - - - +
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Residues in contact with TYR 129 (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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80B ILE* 3.8 12.1 - - + -
81B LYS 3.4 3.8 - - - -
82B GLY* 3.6 20.2 - - - -
83B PRO* 3.6 13.2 - - + +
86B ILE* 4.0 6.5 - - + +
88B PHE* 4.1 19.7 - + - -
120B VAL* 4.8 3.6 - - + -
124B MET* 3.4 12.2 - - + +
125B ALA* 2.5 42.4 + - - -
127B GLY 3.5 17.9 - - - -
128B LYS* 1.3 76.8 - - - +
130B THR* 1.3 62.4 + - - +
131B VAL 4.2 0.2 - - - -
148B GLU* 3.3 8.3 - - - +
149B PHE* 2.8 75.4 + + + +
151B LYS* 4.0 13.0 - - + -
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Residues in contact with THR 130 (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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79B SER 3.9 0.7 - - - +
80B ILE* 3.4 3.8 - - - +
81B LYS* 2.7 46.0 + - - +
128B LYS* 5.5 3.1 - - - +
129B TYR* 1.3 75.3 + - - +
131B VAL* 1.3 71.1 + - - +
132B SER* 5.0 4.0 - - - +
146B ASN* 3.8 26.9 - - + +
147B GLN 3.6 7.4 - - - +
148B GLU* 4.5 13.3 + - + +
1272B O4B 3.9 31.5 - - - -
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Residues in contact with VAL 131 (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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44B LEU* 3.7 20.2 - - + +
46B LEU* 4.3 13.5 - - + -
78B LEU* 3.8 18.4 - - + -
79B SER 3.6 2.5 - - - -
80B ILE* 3.6 16.8 - - + -
118B PHE* 3.6 22.7 - - + -
129B TYR 4.2 0.2 - - - -
130B THR* 1.3 73.4 - - - +
132B SER* 1.3 63.2 - - - +
146B ASN* 3.2 6.6 - - - +
147B GLN 2.7 39.1 + - - +
149B PHE* 3.3 34.3 - - + -
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Residues in contact with SER 132 (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* 5.4 5.6 - - - -
78B LEU* 3.6 5.3 - - - -
79B SER* 2.8 39.5 + - - -
130B THR* 5.1 3.8 - - - -
131B VAL* 1.3 75.2 - - - +
133B LEU* 1.3 60.6 + - - +
134B GLN* 2.8 39.3 + - - +
144B LYS* 4.3 2.8 - - - +
146B ASN* 3.1 27.1 + - - +
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Residues in contact with LEU 133 (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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42B ALA* 4.2 15.3 - - + -
43B ASN 3.2 29.2 - - - +
44B LEU* 3.8 9.1 - - + +
62B LEU* 4.0 24.0 - - + -
63B GLY 3.9 12.8 - - - +
64B ILE* 4.2 9.4 - - + -
76B TYR* 3.9 23.6 - - + -
77B TRP 3.8 10.3 - - - +
78B LEU* 3.7 14.5 - - + +
132B SER* 1.3 71.2 - - - +
134B GLN* 1.3 70.8 + - - +
135B VAL* 4.6 1.1 - - + -
144B LYS* 3.2 8.3 - - - +
145B ALA* 2.8 40.1 + - + +
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Residues in contact with GLN 134 (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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211A GLY 3.1 23.6 + - - -
212A LEU* 3.2 21.6 - - + +
213A ILE* 2.9 33.1 + - - +
75B LYS 4.2 0.2 - - - +
76B TYR* 3.2 4.7 - - - +
77B TRP* 3.0 61.6 + - + +
79B SER* 4.9 1.3 - - - -
132B SER* 2.8 38.0 + - - +
133B LEU* 1.3 74.1 - - - +
135B VAL* 1.3 61.4 + - - +
143B PHE 3.6 4.0 - - - -
144B LYS* 4.0 9.1 - - + +
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Residues in contact with VAL 135 (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* 4.2 21.3 - - + -
42B ALA* 4.3 15.7 - - + -
64B ILE* 3.9 30.5 - - + -
74B PHE* 3.8 36.1 - - + -
75B LYS 3.5 2.2 - - - -
76B TYR* 4.1 1.3 - - + -
133B LEU* 4.6 3.1 - - + -
134B GLN* 1.3 78.1 - - - +
136B VAL* 1.3 67.5 + - - +
137B ALA 4.5 0.9 - - - +
141B LYS 3.8 1.0 - - - +
142B VAL* 3.5 5.0 - - - +
143B PHE* 2.8 48.0 + - + +
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Residues in contact with VAL 136 (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* 4.0 24.2 - - + -
241A SER* 3.5 40.1 + - - +
242A TYR* 4.1 12.3 - - + -
243A PRO* 4.6 3.6 - - + -
74B PHE* 3.4 2.4 - - - -
75B LYS* 2.7 42.4 + - + +
77B TRP* 3.6 33.4 - - + -
134B GLN 4.3 0.2 - - - -
135B VAL* 1.3 75.0 - - - +
137B ALA* 1.3 63.1 + - - +
140B GLY 4.7 3.4 - - - +
141B LYS 3.8 5.4 - - - +
142B VAL* 4.5 4.0 - - + -
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Residues in contact with ALA 137 (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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241A SER* 3.4 7.3 - - - -
39B VAL* 5.8 2.0 - - + -
40B ILE* 4.5 9.6 - - + -
72B VAL* 4.7 8.1 - - + -
73B LYS 4.2 3.8 - - - +
74B PHE* 3.8 12.3 - - + -
135B VAL* 4.0 1.8 - - - +
136B VAL* 1.3 75.3 - - - +
138B GLU* 1.3 54.7 + - - +
139B ASN* 3.0 21.3 - - - +
140B GLY* 2.8 26.9 + - - -
141B LYS 3.1 14.6 + - - +
143B PHE* 4.1 15.0 - - + -
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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