Contacts of the strand formed by residues 116 - 122 (chain A) in PDB entry 2RSY
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A PHE* 3.3 36.9 - + - -
106A VAL* 3.8 14.6 - - + -
107A ARG 3.7 3.1 - - - -
108A GLU* 3.8 27.4 - - + -
109A SER* 4.3 1.4 - - - -
114A GLY 5.2 4.7 - - - -
115A ASP* 1.3 87.3 - - - +
117A THR* 1.3 64.3 + - - +
130A ARG* 3.7 1.2 - - - +
131A ILE* 2.7 44.3 + - + +
133A TYR* 3.5 31.9 - + + -
138A LEU* 4.0 4.7 - - + -
149A LEU* 3.3 31.7 - - + +
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Residues in contact with THR 117 (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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105A LEU 3.4 4.7 - - - +
106A VAL* 3.4 1.5 - - - -
107A ARG* 3.0 55.6 + - - +
109A SER* 3.6 2.1 - - - -
116A TYR* 1.3 79.0 + - - +
118A LEU* 1.3 62.3 + - - +
119A CYS* 3.8 1.1 + - - +
128A HIS* 3.7 20.0 - - + +
129A TYR 3.5 2.9 - - - +
131A ILE* 4.6 2.0 - - - -
314B PTR 2.6 61.2 + - + +
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Residues in contact with LEU 118 (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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104A PHE* 3.7 33.7 - - + -
105A LEU 3.2 5.6 - - - +
106A VAL* 4.2 11.7 - - + +
117A THR* 1.3 71.8 - - - +
119A CYS* 1.3 61.3 + - - +
120A VAL* 3.2 27.1 - - + -
127A GLU 3.0 6.8 - - - +
128A HIS* 3.2 1.6 - - - -
129A TYR* 2.8 67.6 + - + +
131A ILE* 4.3 13.4 - - + +
140A ILE* 5.2 4.3 - - + -
152A LEU* 6.0 2.7 - - + -
153A VAL* 5.5 3.8 - - + -
156A TYR* 5.8 4.9 - - + -
163A LEU* 4.1 15.0 - - + -
167A LEU* 4.6 9.4 - - + -
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Residues in contact with CYS 119 (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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92A ALA* 4.8 9.2 - - + -
96A LEU* 4.5 10.7 - - - +
103A LEU 3.7 0.7 - - - +
104A PHE* 3.2 3.6 - - - -
105A LEU* 2.8 57.5 + - + +
107A ARG* 5.2 2.0 - - - +
117A THR* 3.8 1.7 + - + +
118A LEU* 1.3 71.0 - - - +
120A VAL* 1.3 63.6 + - - +
126A VAL* 3.8 24.9 - - - -
127A GLU 3.3 3.8 - - - -
128A HIS* 3.4 37.2 - - + +
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Residues in contact with VAL 120 (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 LEU* 4.2 2.9 - - - -
102A GLY 4.7 1.1 - - - +
103A LEU 3.2 18.8 - - - +
104A PHE* 3.8 11.9 - - + -
118A LEU* 3.2 32.3 - - + -
119A CYS* 1.3 76.8 - - - +
121A SER* 1.3 67.0 + - - +
122A CYS* 3.8 1.5 + - + +
125A LYS 3.1 3.6 - - - +
126A VAL* 3.3 4.5 - - - -
127A GLU* 2.9 39.4 + - + +
129A TYR* 4.5 6.3 - - + -
163A LEU* 4.9 2.9 - - + -
164A CYS* 6.2 1.6 - - + -
165A THR* 3.7 33.9 - - + +
167A LEU* 4.6 6.5 - - + -
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Residues in contact with SER 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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96A LEU* 2.9 46.6 + - - +
98A PRO 4.2 4.5 + - - -
99A PRO* 4.7 3.9 - - - +
100A GLU 3.4 35.7 - - - +
101A THR* 3.6 11.6 + - - -
103A LEU* 3.2 4.6 + - - -
120A VAL* 1.3 75.9 - - - +
122A CYS* 1.3 60.4 + - - +
123A GLU 3.9 1.3 + - - -
124A GLY 5.0 3.8 - - - -
125A LYS 3.2 6.3 + - - -
126A VAL* 4.5 2.3 - - - +
165A THR* 4.2 3.1 - - - +
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Residues in contact with CYS 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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101A THR* 4.2 7.9 - - - -
120A VAL* 3.8 1.5 + - + +
121A SER* 1.3 70.8 - - - +
123A GLU* 1.3 76.5 + - - +
124A GLY 3.2 0.4 - - - -
125A LYS* 2.7 43.2 + - + +
127A GLU* 4.7 3.1 - - + -
164A CYS* 2.1 53.8 - - + -
165A THR* 3.4 24.9 - - + -
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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