Contacts of the strand formed by residues 155 - 163 (chain A) in PDB entry 2C9A
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 TYR 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PRO 4.0 0.5 - - - +
88A GLN* 3.4 4.7 - - - -
89A LEU* 2.9 49.1 + - + +
91A GLU* 5.6 0.7 - - + -
95A HIS* 2.6 37.8 + + - -
97A ILE* 3.6 15.7 - - + +
118A VAL* 3.7 24.0 - - + -
119A LYS 3.2 13.0 - - - +
120A VAL* 4.2 4.5 - - + -
147A ILE* 3.5 32.9 + - + +
149A THR* 3.7 34.5 - - + -
154A PHE* 1.3 79.2 - - - +
156A GLN* 1.3 62.2 + - - +
157A VAL* 3.8 22.0 - - + -
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Residues in contact with GLN 156 (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 SER* 5.2 2.2 + - - -
85A LEU* 3.6 32.8 - - - +
86A LEU 3.0 29.4 + - - +
87A PRO* 4.4 2.4 - - - +
88A GLN* 3.7 34.9 - - + +
117A TYR 3.5 0.9 - - - +
118A VAL* 3.4 5.5 - - - -
119A LYS* 2.9 48.6 + - + +
155A TYR* 1.3 74.3 - - - +
157A VAL* 1.3 64.9 + - - +
158A ILE* 3.7 15.8 + - - +
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Residues in contact with VAL 157 (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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85A LEU* 3.6 0.2 - - - -
86A LEU* 2.8 61.1 + - + +
87A PRO 4.9 0.2 + - - -
89A LEU* 5.6 0.4 - - + -
97A ILE* 3.6 29.8 - - + -
116A VAL* 3.8 23.3 - - + -
117A TYR 3.4 3.6 - - - -
118A VAL* 4.1 9.6 - - + -
145A LEU* 4.2 12.6 - - + -
155A TYR* 3.8 17.0 + - + -
156A GLN* 1.3 72.7 - - - +
158A ILE* 1.3 64.4 + - - +
159A PHE* 4.3 11.2 - - + -
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Residues in contact with ILE 158 (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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83A HIS* 3.6 28.9 - - + -
84A LEU 3.6 2.9 - - - -
85A LEU* 3.1 36.8 - - + -
116A VAL* 3.5 4.6 - - - -
117A TYR* 2.9 46.7 + - + +
119A LYS* 3.8 16.4 - - + +
125A LEU* 3.4 28.0 - - + -
156A GLN* 3.9 23.6 - - - +
157A VAL* 1.3 79.7 - - - +
159A PHE* 1.3 63.2 + - - +
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Residues in contact with PHE 159 (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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38A TYR* 5.0 0.9 - + - -
48A TRP* 3.9 6.6 - - + -
82A ALA 3.4 1.6 - - - +
83A HIS* 3.1 5.0 - - - -
84A LEU* 2.7 64.3 + - + +
86A LEU* 3.5 28.5 - - + -
97A ILE* 5.8 0.4 - - + -
99A PHE* 3.8 44.2 - + + -
114A LEU* 4.3 7.9 - - + -
115A ASN 3.6 1.6 - - - -
116A VAL* 3.6 30.1 - - + -
145A LEU* 5.5 0.2 - - + -
157A VAL* 4.3 9.2 - - + -
158A ILE* 1.3 71.2 - - - +
160A GLU* 1.3 60.2 + - - +
161A VAL 4.2 0.2 - - - -
172A ILE* 3.9 26.7 - - + -
175A VAL* 4.0 14.8 - - + -
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Residues in contact with GLU 160 (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 ARG* 3.3 23.2 + - + -
82A ALA 3.4 6.1 - - - +
83A HIS* 3.0 38.7 + - + +
114A LEU* 3.6 2.9 - - - +
115A ASN* 2.8 55.9 + - - +
117A TYR* 2.6 41.5 + - + -
125A LEU* 5.5 0.7 - - - +
159A PHE* 1.3 72.9 - - - +
161A VAL* 1.3 65.7 + - - +
162A ILE* 3.6 18.6 + - + +
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Residues in contact with VAL 161 (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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46A PHE* 4.9 1.3 - - + -
48A TRP* 3.2 32.7 - - + -
71A VAL* 3.7 34.5 - - + -
80A GLN 3.4 1.2 - - - +
81A ARG* 3.3 4.9 - - - -
82A ALA* 3.0 35.1 + - + +
112A GLY* 4.9 0.2 - - - -
113A LEU 3.4 9.4 - - - +
114A LEU* 4.3 5.2 - - + -
160A GLU* 1.3 73.6 - - - +
162A ILE* 1.3 71.9 + - - +
163A THR* 4.2 8.3 - - + +
170A LEU* 4.1 27.8 - - + -
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Residues in contact with ILE 162 (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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78A GLU* 4.2 8.3 - - - +
79A GLY* 3.7 22.7 - - - +
80A GLN 3.2 6.3 - - - +
81A ARG* 3.8 26.5 - - + +
113A LEU* 2.8 61.4 + - + +
115A ASN* 4.0 11.0 - - - +
160A GLU* 3.6 29.6 - - - +
161A VAL* 1.3 79.0 - - - +
163A THR* 1.3 73.5 + - - +
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Residues in contact with THR 163 (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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46A PHE* 4.2 18.8 - - + -
71A VAL* 4.8 1.1 - - + -
73A ALA* 4.6 9.9 - - + -
76A ARG* 4.2 22.9 - - + -
77A PRO 2.4 29.1 + - - -
78A GLU* 3.3 3.3 - - - +
79A GLY 3.0 24.3 + - - -
80A GLN* 3.0 22.4 + - + +
111A PRO 3.6 11.4 - - - +
112A GLY* 4.0 0.7 - - - -
161A VAL* 4.5 7.4 - - + -
162A ILE* 1.3 78.6 - - - +
164A SER* 1.3 59.9 + - - +
165A GLY 4.2 3.4 - - - -
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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