Contacts of the strand formed by residues 120 - 130 (chain B) in PDB entry 6YB9
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 LYS 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A GLY 5.7 0.8 + - - -
319A ASP* 5.7 5.3 - - - +
102B ARG* 3.4 14.8 - - + +
103B ILE* 3.9 31.2 - - + -
118B GLY 3.3 11.6 + - - +
119B TYR* 1.3 90.4 + - - +
121B PHE* 1.3 60.0 + - - +
122B TYR* 3.7 44.1 + - + +
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Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B ARG* 3.7 37.2 - - + +
102B ARG* 2.9 46.2 + - - -
104B ALA* 3.6 30.1 - - + -
108B PHE* 3.6 45.5 - + - -
119B TYR* 4.0 21.8 - + - -
120B LYS* 1.3 70.7 - - - +
122B TYR* 1.3 59.4 + - - +
123B PRO 3.3 16.9 - - - +
124B PRO 3.6 0.7 - - - -
125B LYS* 3.8 28.9 - - + +
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Residues in contact with TYR 122 (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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311A ARG* 4.2 15.8 + - - +
314A ALA* 3.8 17.3 - - - +
315A GLU* 4.0 41.7 - - + +
318A GLY* 3.6 25.8 - - - -
319A ASP* 4.1 12.7 - - + +
102B ARG* 3.7 16.8 - - - -
120B LYS* 3.7 48.0 + - + +
121B PHE* 1.3 72.6 - - - +
123B PRO* 1.4 62.9 + - - +
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Residues in contact with PRO 123 (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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310A LEU 6.0 0.2 - - - +
311A ARG* 4.9 9.6 - - + -
314A ALA* 3.7 21.5 - - + +
102B ARG* 4.6 0.7 - - - +
121B PHE* 3.3 12.7 - - - +
122B TYR* 1.4 84.2 + - - +
124B PRO* 1.4 79.6 - - + +
125B LYS* 3.4 2.1 + - - -
170B GLN* 3.9 22.0 - - - +
174B GLU* 5.7 0.7 - - - +
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Residues in contact with PRO 124 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B CYS* 3.4 24.0 - - - -
101B ARG 3.2 13.0 - - - +
102B ARG* 3.5 33.7 - - - +
121B PHE 3.6 5.4 - - - +
123B PRO* 1.4 90.9 - - + +
125B LYS* 1.3 62.0 + - - +
126B VAL* 3.7 1.4 + - - +
170B GLN* 2.9 32.9 + - + -
173B PHE* 4.1 15.7 - - + -
174B GLU* 4.2 14.6 - - + +
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B VAL 3.6 0.9 - - - +
100B CYS* 3.1 5.7 - - - -
101B ARG* 2.8 40.5 + - + +
108B PHE* 4.4 12.3 - - + -
121B PHE* 3.8 41.6 - - + +
123B PRO 3.4 2.7 + - - -
124B PRO* 1.3 70.0 - - - +
126B VAL* 1.3 68.1 + - - +
127B GLU* 4.0 26.4 - - + +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B TRP* 4.1 17.3 - - + -
99B VAL 3.2 8.1 - - - +
100B CYS* 4.2 7.9 - - - -
124B PRO 3.7 6.7 + - - +
125B LYS* 1.3 82.9 - - - +
127B GLU* 1.3 69.4 - - - +
128B LEU* 5.1 4.2 - - + +
166B SER* 3.7 39.9 - - - +
169B THR* 4.1 11.4 - - + -
170B GLN* 4.2 24.7 - - + +
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Residues in contact with GLU 127 (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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97B GLU 3.7 0.7 - - - +
98B TRP* 3.5 4.5 - - - -
99B VAL* 2.8 36.3 + - + +
101B ARG* 2.9 38.2 + - + +
108B PHE* 3.5 17.1 - - - -
111B ARG* 2.6 33.7 + - - -
125B LYS* 4.0 13.9 - - + +
126B VAL* 1.3 79.8 - - - +
128B LEU* 1.3 66.3 - - - +
129B PHE* 3.7 14.2 - - + -
139B GLN* 3.8 16.7 + - - +
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Residues in contact with LEU 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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96B ILE* 4.1 8.7 - - + -
97B GLU 3.5 4.5 - - - -
98B TRP* 3.6 31.0 - - + +
126B VAL* 5.1 4.5 - - + +
127B GLU* 1.3 79.2 - - - +
129B PHE* 1.3 63.8 + - - +
139B GLN* 3.4 10.8 - - - +
140B TRP* 3.0 40.5 + - + +
141B SER 4.3 9.4 - - - +
142B GLU* 4.4 24.7 - - + +
145B LEU* 3.5 41.1 - - + -
166B SER* 5.5 1.1 - - - +
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Residues in contact with PHE 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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96B ILE* 3.3 6.8 - - - +
97B GLU* 2.6 59.4 + - + +
99B VAL* 3.7 23.6 - - + -
101B ARG* 4.1 4.9 - - - -
107B SER* 4.3 4.3 - - - -
111B ARG* 3.7 32.8 - - - -
127B GLU* 3.7 31.2 - - + -
128B LEU* 1.3 74.3 - - - +
130B PHE* 1.3 62.6 + - - +
131B LYS 3.7 0.2 + - - -
137B ASP* 3.4 32.5 - - + +
138B PRO 3.5 3.1 - - - -
139B GLN* 3.7 25.6 - - + -
703B OK8 4.5 4.3 - + - -
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Residues in contact with PHE 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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95B PRO* 3.6 24.5 - - + -
96B ILE* 3.9 5.3 - - + +
128B LEU 4.4 0.2 - - - -
129B PHE* 1.3 70.8 - - - +
131B LYS* 1.3 71.2 + - - +
132B ASP* 3.5 27.0 + - + -
137B ASP* 3.3 26.0 - - - +
138B PRO* 3.1 18.9 + - + +
140B TRP* 3.4 59.9 - + + +
150B PHE* 4.1 19.1 - + - -
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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