Contacts of the strand formed by residues 127 - 137 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A PRO* 4.2 5.8 - - - -
125A ALA 3.7 1.4 + - - -
126A ASP* 1.3 74.5 - - - +
128A LYS* 1.3 63.0 + - - -
129A TYR* 3.5 7.6 - - - -
150A VAL* 3.4 2.8 - - - -
151A LYS 2.8 36.9 + - - -
153A VAL* 4.3 17.4 - - - +
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Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LYS 4.4 0.3 - - - +
82A GLY* 3.9 2.6 - - - -
83A PRO* 3.5 23.7 - - - +
127A GLY* 1.3 71.2 - - - -
129A TYR* 1.3 69.9 + - - +
130A THR* 5.5 2.2 - - - +
148A GLU* 4.6 20.6 - - + +
149A PHE 3.9 6.5 - - - +
150A VAL* 4.3 12.8 - - + -
153A VAL* 4.9 0.8 - - + +
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Residues in contact with TYR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 3.8 12.6 - - + -
81A LYS 3.4 3.6 - - - -
82A GLY* 3.6 19.5 - - - -
83A PRO* 3.6 14.3 - - + +
86A ILE* 4.2 6.6 - - + +
88A PHE* 4.1 19.3 - + - -
120A VAL* 4.8 4.5 - - + -
124A MET* 3.4 11.6 - - + +
125A ALA* 2.4 43.1 + - - -
127A GLY 3.5 17.0 - - - -
128A LYS* 1.3 77.2 - - - +
130A THR* 1.3 63.6 + - - +
131A VAL 4.1 0.2 - - - -
148A GLU* 3.3 8.5 - - - +
149A PHE* 2.8 73.9 + + + +
151A LYS* 4.0 13.7 - - + -
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Residues in contact with THR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER 3.9 0.5 - - - +
80A ILE* 3.5 3.5 - - - -
81A LYS* 2.7 50.5 + - + +
128A LYS* 5.5 2.6 + - - +
129A TYR* 1.3 73.9 + - - +
131A VAL* 1.3 71.2 + - - +
132A SER* 5.0 3.7 - - - -
146A ASN* 3.8 26.7 - - + +
147A GLN 3.6 7.2 - - - +
148A GLU* 4.5 14.8 + - + +
1272A O4B 4.0 28.2 - - - +
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.7 19.8 - - + +
46A LEU* 4.3 12.1 - - + -
78A LEU* 3.8 17.7 - - + -
79A SER 3.6 2.9 - - - +
80A ILE* 3.7 18.4 - - + -
118A PHE* 3.6 22.4 - - + -
130A THR* 1.3 74.2 - - - +
132A SER* 1.3 62.6 + - - +
146A ASN* 3.2 6.1 - - - +
147A GLN 2.7 39.6 + - - +
149A PHE* 3.3 35.7 - - + -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.7 4.7 - - - -
79A SER* 2.8 39.2 + - - -
130A THR* 5.0 4.5 - - - -
131A VAL* 1.3 74.3 - - - +
133A LEU* 1.3 61.7 + - - +
134A GLN* 2.8 40.8 + - - +
144A LYS* 4.4 2.4 - - - +
146A ASN* 3.0 27.5 + - - +
1272A O4B 6.3 2.2 - - - -
213B ILE* 5.3 6.1 - - - -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 4.2 14.6 - - + -
43A ASN 3.2 28.0 - - - +
44A LEU* 3.7 9.3 - - + +
62A LEU* 4.0 25.1 - - + -
63A GLY 3.9 13.7 - - - +
64A ILE* 4.2 9.6 - - + -
76A TYR* 3.9 23.6 - - + -
77A TRP 3.8 9.9 - - - +
78A LEU* 3.7 14.0 - - + +
132A SER* 1.3 71.0 - - - +
134A GLN* 1.3 69.8 + - - +
135A VAL* 4.6 1.8 - - + -
144A LYS* 3.2 7.6 - - - +
145A ALA 2.8 41.6 + - - +
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Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS 4.2 0.2 - - - +
76A TYR* 3.2 5.4 - - - +
77A TRP* 3.0 60.1 + - + +
79A SER* 5.0 0.7 - - - -
132A SER* 2.8 39.0 + - - +
133A LEU* 1.3 74.8 - - - +
135A VAL* 1.3 62.8 + - - +
143A PHE 3.6 3.6 - - - -
144A LYS* 4.0 9.7 - - + +
1272A O4B 5.6 0.4 - - - -
211B GLY 3.0 24.6 + - - -
212B LEU* 3.4 19.3 - - + +
213B ILE* 2.9 33.1 + - - +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 4.2 21.5 - - + -
42A ALA* 4.2 14.8 - - + -
64A ILE* 3.9 31.2 - - + -
74A PHE* 3.8 35.2 - - + -
75A LYS 3.5 2.9 - - - -
76A TYR* 4.1 0.9 - - + -
133A LEU* 4.6 3.8 - - + -
134A GLN* 1.3 78.7 - - - +
136A VAL* 1.3 67.5 + - - +
137A ALA 4.5 0.7 - - - +
141A LYS 3.8 0.9 - - - +
142A VAL* 3.5 4.9 - - - +
143A PHE* 2.8 48.7 + - + +
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 4.1 2.0 - - - -
75A LYS* 2.7 44.0 + - + +
77A TRP* 3.7 31.6 - - + -
135A VAL* 1.3 76.2 - - - +
137A ALA* 1.3 69.9 + - - +
140A GLY 4.6 5.8 - - - +
141A LYS 3.8 5.6 - - - +
142A VAL* 4.5 6.5 - - + -
212B LEU* 4.0 23.6 - - + -
241B SER* 4.0 30.0 + - - +
242B TYR* 4.3 13.0 - - + -
243B PRO* 4.9 0.7 - - + -
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 5.8 1.8 - - + -
40A ILE* 4.5 9.2 - - + -
72A VAL* 4.7 8.1 - - + -
73A LYS 4.2 4.3 - - - +
74A PHE* 3.8 13.7 - - + -
135A VAL* 4.0 2.0 - - - +
136A VAL* 1.3 75.4 - - - +
138A GLU* 1.3 54.7 + - - +
139A ASN* 3.0 21.5 - - - +
140A GLY* 2.8 27.2 + - - -
141A LYS 3.1 14.0 + - - +
143A PHE* 4.1 15.0 - - + -
241B SER* 3.9 6.6 - - - -
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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