Contacts of the strand formed by residues 127 - 137 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D PRO* 4.2 5.8 - - - -
125D ALA 3.7 1.0 + - - -
126D ASP* 1.3 74.6 - - - +
128D LYS* 1.3 63.1 + - - -
129D TYR* 3.5 7.7 - - - -
150D VAL* 3.4 2.8 - - - -
151D LYS* 2.8 36.5 + - - +
153D VAL* 4.3 17.9 - - - +
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LYS 4.4 0.3 - - - +
82D GLY* 3.9 2.4 - - - -
83D PRO* 3.5 22.6 - - - +
127D GLY* 1.3 70.8 - - - -
129D TYR* 1.3 62.6 + - - +
148D GLU* 6.2 4.9 - - + +
149D PHE 3.9 4.5 - - - +
150D VAL* 4.3 12.3 - - + -
153D VAL* 4.9 0.8 - - + +
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Residues in contact with TYR 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ILE* 3.8 12.8 - - + -
81D LYS 3.4 3.6 - - - -
82D GLY* 3.6 20.4 - - - -
83D PRO* 3.6 13.6 - - + +
86D ILE* 4.0 6.8 - - + +
88D PHE* 4.1 18.8 - + - -
120D VAL* 4.8 4.3 - - + -
124D MET* 3.4 12.2 - - + +
125D ALA* 2.5 42.4 + - - -
127D GLY 3.5 16.6 - - - -
128D LYS* 1.3 76.1 - - - +
130D THR* 1.3 62.5 + - - +
131D VAL 4.2 0.4 - - - -
148D GLU* 3.3 9.1 - - - +
149D PHE* 2.8 73.4 + + + +
151D LYS* 4.0 13.9 - - + -
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Residues in contact with THR 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D SER 3.9 0.7 - - - +
80D ILE* 3.5 3.2 - - - -
81D LYS* 2.7 46.3 + - - +
128D LYS 5.6 0.3 - - - -
129D TYR* 1.3 74.5 + - - +
131D VAL* 1.3 70.7 + - - +
132D SER* 5.0 3.7 - - - -
146D ASN* 3.8 27.1 - - + +
147D GLN 3.6 7.9 - - - +
148D GLU* 4.5 13.6 + - + +
1272D O4B 3.8 30.9 - - - -
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Residues in contact with VAL 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 3.7 20.2 - - + +
46D LEU* 4.3 13.5 - - + -
78D LEU* 3.8 18.8 - - + -
79D SER 3.6 2.7 - - - -
80D ILE* 3.7 16.6 - - + -
118D PHE* 3.6 22.4 - - + -
129D TYR 4.2 0.2 - - - -
130D THR* 1.3 71.5 - - - +
132D SER* 1.3 63.1 + - - +
146D ASN* 3.2 6.9 - - - +
147D GLN 2.7 39.7 + - - +
149D PHE* 3.3 35.2 - - + -
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Residues in contact with SER 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ILE* 5.3 5.4 - - - -
78D LEU* 3.7 5.1 - - - -
79D SER* 2.8 39.2 + - - -
130D THR* 5.0 4.5 - - - -
131D VAL* 1.3 76.3 - - - +
133D LEU* 1.3 60.4 + - - +
134D GLN* 2.8 39.0 + - - +
144D LYS* 4.4 2.6 - - - +
146D ASN* 3.0 26.3 + - - +
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Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA* 4.2 15.5 - - + -
43D ASN 3.1 28.7 - - - +
44D LEU* 3.7 10.4 - - + +
62D LEU* 4.0 24.7 - - + -
63D GLY 3.9 13.0 - - - +
64D ILE* 4.2 9.2 - - + -
76D TYR* 3.9 24.0 - - + -
77D TRP 3.8 9.9 - - - +
78D LEU* 3.7 14.7 - - + +
132D SER* 1.3 71.3 - - - +
134D GLN* 1.3 69.6 + - - +
135D VAL* 4.6 1.3 - - + -
144D LYS* 3.2 7.8 - - - +
145D ALA 2.8 39.4 + - - +
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Residues in contact with GLN 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C GLY 3.0 24.7 + - - -
212C LEU* 3.4 19.6 - - + +
213C ILE* 2.9 32.6 + - - +
76D TYR* 3.2 5.4 - - - +
77D TRP* 3.0 59.4 + - + +
79D SER* 5.0 1.3 - - - -
132D SER* 2.8 38.0 + - - +
133D LEU* 1.3 74.6 - - - +
135D VAL* 1.3 61.8 + - - +
136D VAL 4.3 0.2 - - - -
143D PHE 3.6 3.8 - - - -
144D LYS* 4.0 9.7 - - + +
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Residues in contact with VAL 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ILE* 3.9 39.5 - - + -
42D ALA* 4.2 7.4 - - + -
64D ILE* 3.9 27.6 - - + -
74D PHE* 3.8 35.2 - - + -
75D LYS 3.5 2.9 - - - +
76D TYR* 4.1 2.0 - - + -
133D LEU* 4.6 2.9 - - + -
134D GLN* 1.3 77.4 - - - +
136D VAL* 1.3 66.0 + - - +
137D ALA 4.5 0.2 - - - +
141D LYS 3.8 0.9 - - - +
142D VAL* 3.5 5.0 - - - +
143D PHE* 2.8 42.9 + - + +
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Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C LEU* 4.0 22.9 - - + -
241C SER* 4.0 28.9 + - - +
242C TYR* 4.3 13.7 - - + -
243C PRO* 4.9 1.1 - - + -
74D PHE* 3.4 1.7 - - - -
75D LYS* 2.7 43.6 + - + +
77D TRP* 3.7 32.3 - - + -
134D GLN 4.3 0.2 - - - -
135D VAL* 1.3 75.8 - - - +
137D ALA* 1.3 70.2 + - - +
140D GLY 4.6 6.1 - - - +
141D LYS 3.8 5.2 - - - +
142D VAL* 4.5 6.3 - - + -
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C SER* 3.9 6.4 - - - -
38D PRO* 5.4 2.7 - - + +
40D ILE* 4.9 4.3 - - + -
72D VAL* 4.7 11.2 - - + -
73D LYS 4.2 3.8 - - - +
74D PHE* 3.8 12.3 - - + +
135D VAL 4.0 1.6 - - - -
136D VAL* 1.3 75.9 - - - +
138D GLU* 1.3 55.3 + - - +
139D ASN* 3.0 21.3 - - - +
140D GLY* 2.8 27.2 + - - -
141D LYS 3.1 14.3 + - - +
143D PHE* 4.1 15.3 - - + -
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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