Contacts of the strand formed by residues 120 - 130 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ARG* 3.4 13.3 - - + +
103A ILE* 3.7 36.7 - - + +
118A GLY 3.6 13.2 - - - +
119A TYR* 1.3 92.4 - - - +
121A PHE* 1.3 62.2 + - - +
122A TYR* 3.7 46.6 + - + +
186A THR* 5.5 2.4 - - - +
318B GLY 5.5 2.2 - - - -
319B ASP* 6.0 2.2 - - - +
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Residues in contact with PHE 121 (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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101A ARG* 3.6 42.2 - - + +
102A ARG* 2.9 43.5 + - - +
104A ALA* 3.6 28.7 - - + -
108A PHE* 3.5 45.5 - + - -
119A TYR* 4.0 22.7 - + - -
120A LYS* 1.3 70.2 - - - +
122A TYR* 1.3 61.2 + - - +
123A PRO 3.3 17.5 - - - +
124A PRO 3.6 0.5 - - - -
125A LYS* 3.8 25.1 - - + +
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Residues in contact with TYR 122 (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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102A ARG* 3.7 13.0 - - - +
120A LYS* 3.7 47.2 + - + +
121A PHE* 1.3 76.7 - - - +
123A PRO* 1.4 62.5 + - - +
311B ARG* 4.1 15.7 + - - +
314B ALA* 3.9 16.2 - - - +
315B GLU* 3.9 40.4 - - + +
318B GLY* 3.5 25.4 - - - -
319B ASP* 3.9 16.3 - - + +
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Residues in contact with PRO 123 (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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102A ARG* 4.6 0.9 - - - +
121A PHE* 3.3 14.0 - - - +
122A TYR* 1.4 82.2 - - - +
124A PRO* 1.4 80.2 - - + +
125A LYS* 3.3 2.6 + - - -
170A GLN* 3.9 20.2 - - - +
174A GLU* 5.4 0.4 - - - +
310B LEU 5.9 0.2 - - - +
311B ARG* 4.8 10.8 - - + -
313B LYS* 6.4 0.2 - - - +
314B ALA* 3.6 22.8 - - + -
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Residues in contact with PRO 124 (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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100A CYS* 3.4 24.0 - - - -
101A ARG 3.2 13.9 - - - +
102A ARG* 3.5 33.9 - - - +
121A PHE 3.6 5.1 - - - +
123A PRO* 1.4 90.5 - - + +
125A LYS* 1.3 62.5 + - - +
126A VAL* 3.7 0.9 + - - +
170A GLN* 2.9 26.7 + - + +
173A PHE* 4.1 8.7 - - + -
174A GLU* 4.0 28.9 - - + +
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Residues in contact with LYS 125 (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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99A VAL 3.7 0.7 - - - +
100A CYS* 3.1 5.9 - - - -
101A ARG* 2.8 39.6 + - + +
108A PHE* 4.4 11.8 - - + -
121A PHE* 3.8 42.0 - - + +
123A PRO 3.3 3.7 + - - +
124A PRO* 1.3 70.0 - - - +
126A VAL* 1.3 66.0 + - - +
127A GLU* 4.2 27.2 + - + +
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Residues in contact with VAL 126 (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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98A TRP* 4.1 22.2 - - + -
99A VAL 3.2 9.4 - - - +
100A CYS* 4.2 9.9 - - - -
124A PRO 3.7 4.6 + - - +
125A LYS* 1.3 80.0 - - - +
127A GLU* 1.3 70.3 + - - +
128A LEU* 5.2 3.3 - - + +
166A SER* 3.8 40.2 - - - +
169A THR* 4.2 6.5 - - + -
170A GLN* 4.1 25.1 - - + +
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Residues in contact with GLU 127 (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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97A GLU 3.7 0.5 - - - +
98A TRP* 3.6 4.7 - - - -
99A VAL* 2.8 36.5 + - + +
101A ARG* 2.9 41.0 + - - +
108A PHE* 3.5 16.3 - - - -
111A ARG* 2.6 31.2 + - - -
125A LYS* 4.2 18.4 - - + +
126A VAL* 1.3 79.6 - - - +
128A LEU* 1.3 66.2 + - - +
129A PHE* 3.7 13.7 - - + -
139A GLN* 3.8 14.1 + - - +
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Residues in contact with LEU 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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96A ILE* 4.1 11.2 - - + -
97A GLU 3.5 4.5 - - - -
98A TRP* 3.7 33.2 - - + +
126A VAL* 5.2 3.8 - - + +
127A GLU* 1.3 78.2 - - - +
129A PHE* 1.3 65.1 + - - +
139A GLN* 3.4 10.1 - - - +
140A TRP* 2.9 39.4 + - + +
141A SER 4.3 8.7 - - - +
142A GLU* 4.4 22.2 - - + +
145A LEU* 3.5 41.5 - - + -
166A SER* 5.6 0.9 - - - +
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Residues in contact with PHE 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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96A ILE* 3.3 6.0 - - - +
97A GLU* 2.7 58.2 + - + +
99A VAL* 3.7 23.3 - - + -
101A ARG* 4.1 5.2 - - - -
107A SER* 4.4 4.3 - - - -
111A ARG* 3.7 32.8 - - - -
127A GLU* 3.7 30.7 - - + -
128A LEU* 1.3 75.0 - - - +
130A PHE* 1.3 62.9 + - - +
131A LYS 3.7 0.2 + - - -
137A ASP* 3.5 30.7 - - + +
138A PRO 3.5 3.8 - - - -
139A GLN* 3.7 24.9 - - + -
140A TRP 4.4 0.2 - - - +
502A OK8 4.5 4.7 - + - -
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Residues in contact with PHE 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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95A PRO* 3.6 22.7 - - + -
96A ILE* 3.9 5.7 - - + +
129A PHE* 1.3 71.3 - - - +
131A LYS* 1.3 70.9 + - - +
132A ASP* 3.5 27.9 + - + -
137A ASP* 3.3 25.4 - - - -
138A PRO* 3.1 19.0 + - + +
140A TRP* 3.4 59.6 - + + +
150A PHE* 4.0 22.0 - + - -
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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