Contacts of the strand formed by residues 113 - 124 (chain A) in PDB entry 2I9W
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 HIS 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A PRO 3.5 5.5 - - - +
109A LEU* 3.0 39.8 + - + -
110A SER* 2.8 31.7 + - - +
112A ARG* 1.3 96.3 - - + +
114A ALA* 1.3 60.9 + - - +
136A THR* 4.2 1.8 - - + -
137A PHE 3.2 15.9 - - - +
138A VAL* 3.7 13.7 - - + +
150A TRP* 4.1 3.4 - - - -
153A LEU* 4.0 9.6 - - + -
178A CYS* 3.9 22.4 - - - -
179A CYS* 3.3 26.3 - - - -
182A TYR* 3.5 27.2 - + + -
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Residues in contact with ALA 114 (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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52A ALA* 3.6 26.2 - - + -
105A HIS* 4.7 0.2 - - - +
106A THR 3.2 15.7 - - - +
107A PRO* 3.7 11.4 - - + +
109A LEU* 4.0 3.8 - - - -
113A HIS* 1.3 75.6 - - - +
115A GLN* 1.3 62.1 + - - +
136A THR* 3.5 4.9 - - - +
137A PHE* 2.9 32.4 + - - +
150A TRP* 3.6 17.0 - - + -
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Residues in contact with GLN 115 (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 HIS* 3.4 3.7 - - - -
106A THR* 2.8 49.4 + - - +
109A LEU* 3.6 34.8 - - + +
114A ALA* 1.3 72.3 - - - +
116A VAL* 1.3 68.1 + - - +
117A GLU 4.3 0.2 - - - -
134A LEU* 3.7 37.4 + - + +
135A SER 3.2 15.0 - - - +
136A THR* 3.0 21.9 + - - +
137A PHE* 4.6 0.2 - - - -
182A TYR* 4.3 10.3 + - - +
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Residues in contact with VAL 116 (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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52A ALA* 3.6 4.7 - - + +
53A GLU* 3.6 34.3 - - + +
56A MSE 4.2 15.9 - - + -
102A VAL* 4.1 21.1 - - + -
104A ALA 3.4 10.5 - - - +
105A HIS* 3.9 5.2 - - + -
115A GLN* 1.3 80.2 - - - +
117A GLU* 1.3 63.9 + - - +
118A PHE* 3.8 15.0 - - + -
134A LEU* 3.7 3.3 - - - -
135A SER* 2.9 29.6 + - - -
137A PHE* 3.6 23.6 - - + -
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Residues in contact with GLU 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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102A VAL* 3.7 2.6 - - - +
103A VAL* 2.8 45.3 + - + +
104A ALA* 2.9 29.2 + - + +
115A GLN 4.3 0.2 - - - -
116A VAL* 1.3 72.0 - - - +
118A PHE* 1.3 65.3 + - - +
132A HIS* 2.7 35.5 + - - +
133A GLU 3.3 10.8 - - - +
134A LEU* 3.9 19.9 - - + +
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Residues in contact with PHE 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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56A MSE 2.7 53.8 - - + -
60A TYR* 6.0 2.7 - + + -
100A LEU* 3.7 24.0 - - + -
101A GLU 3.2 13.5 - - - +
102A VAL* 4.1 6.7 - - + -
103A VAL* 4.0 2.9 - - - +
116A VAL* 3.8 15.7 - - + -
117A GLU* 1.3 76.2 - - - +
119A LYS* 1.3 64.5 + - - +
120A ALA* 4.0 18.6 - - + -
132A HIS* 3.5 5.3 - - - -
133A GLU* 2.9 65.3 + - + +
135A SER* 3.5 7.6 - - - -
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Residues in contact with LYS 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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100A LEU* 3.5 5.0 - - - +
101A GLU* 2.8 56.0 + - - +
103A VAL* 4.3 11.0 - - + -
118A PHE* 1.3 80.1 - - - +
120A ALA* 1.3 59.6 - - - +
121A TYR* 3.7 24.4 - - + +
130A ALA* 4.2 11.7 - - + -
131A HIS 3.3 5.2 - - - +
132A HIS* 4.0 38.6 + - + -
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Residues in contact with ALA 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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60A TYR* 4.3 13.9 - - + -
97A TRP* 4.2 21.5 - - + -
99A GLY 3.6 5.2 - - - -
100A LEU* 4.5 1.8 - - + -
118A PHE* 4.0 20.0 - - + -
119A LYS* 1.3 72.3 - - - +
121A TYR* 1.3 61.2 + - - +
122A PHE* 3.8 0.6 - - - -
130A ALA* 3.3 1.4 - - - -
131A HIS* 2.8 48.5 + - + +
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Residues in contact with TYR 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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13A ASN* 4.7 0.2 - - - -
14A PRO* 3.6 32.3 - - + -
15A ALA* 3.8 10.2 - - + +
97A TRP* 3.7 8.5 - - - -
98A ALA* 2.9 35.5 + - + -
99A GLY 2.8 23.3 + - - +
101A GLU* 2.5 38.1 + - + -
119A LYS* 3.7 29.5 - - + +
120A ALA* 1.3 73.3 - - - +
122A PHE* 1.3 64.7 + - - +
128A LEU* 4.2 14.4 - - + -
129A GLN 3.2 15.7 - - - +
130A ALA* 3.8 12.1 - - + +
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Residues in contact with PHE 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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95A THR* 3.8 24.5 - - + -
96A ASP 3.2 13.9 - - - +
97A TRP* 4.7 0.4 - + + -
98A ALA* 3.9 4.0 - - - +
120A ALA 3.8 2.0 - - - -
121A TYR* 1.3 78.7 - - - +
123A LYS* 1.3 65.5 + - - +
124A THR* 3.4 30.1 - - + -
127A GLY 3.8 0.2 - - - +
128A LEU* 3.6 2.9 - - - -
129A GLN* 2.8 54.5 + - + -
130A ALA 4.1 2.7 - - - -
131A HIS* 3.1 56.8 - + - -
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Residues in contact with LYS 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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96A ASP* 2.8 47.0 + - - +
98A ALA* 4.2 8.1 - - + -
122A PHE* 1.3 76.4 - - - +
124A THR* 1.3 68.9 + - - +
127A GLY 3.7 4.9 - - - +
128A LEU* 3.3 29.2 - - + -
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Residues in contact with THR 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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122A PHE* 3.4 33.9 - - + -
123A LYS* 1.3 77.4 - - - +
125A PRO* 1.4 79.1 - - + +
126A ASP* 3.5 13.6 + - - -
127A GLY* 3.0 31.7 + - - +
129A GLN* 3.4 14.4 + - + +
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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