Contacts of the strand formed by residues 127 - 141 (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 GLY 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LYS* 4.6 3.1 - - - -
124A THR* 3.0 37.7 + - - -
125A PRO 3.4 0.9 - - - -
126A ASP* 1.3 78.9 - - - +
128A LEU* 1.3 65.2 + - - -
129A GLN* 3.5 4.1 + - - +
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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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14A PRO* 4.1 31.9 - - + -
98A ALA* 3.8 16.8 - - + -
121A TYR* 4.2 14.8 - - + -
122A PHE 3.6 3.4 - - - +
123A LYS* 3.3 30.5 - - + -
127A GLY* 1.3 69.9 - - - -
129A GLN* 1.3 63.6 + - - +
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Residues in contact with GLN 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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121A TYR* 3.2 9.7 - - - +
122A PHE* 2.8 53.1 + - + +
124A THR* 3.4 34.0 + - + +
126A ASP* 3.9 18.6 - - - +
127A GLY 3.6 4.7 + - - +
128A LEU* 1.3 77.5 + - - +
130A ALA* 1.3 61.5 + - - +
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Residues in contact with ALA 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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119A LYS* 4.2 22.7 - - + -
120A ALA 3.3 7.9 - - - +
121A TYR* 3.8 25.4 - - + -
122A PHE* 4.1 6.1 - - - -
129A GLN* 1.3 77.4 + - - +
131A HIS* 1.3 60.7 + - - +
132A HIS* 3.8 3.1 + - + +
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Residues in contact with HIS 131 (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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91A TRP* 4.7 17.6 + + - -
95A THR* 5.2 2.8 - - - +
97A TRP* 4.5 17.5 - + - -
118A PHE 3.5 2.3 - - - +
119A LYS* 3.3 4.0 - - - -
120A ALA* 2.8 39.6 + - + +
122A PHE* 3.1 42.6 - + - -
130A ALA* 1.3 70.1 + - - +
132A HIS* 1.3 61.2 - - - +
133A GLU* 3.4 27.3 + - + +
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Residues in contact with HIS 132 (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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103A VAL* 4.6 1.8 - - + +
117A GLU* 2.7 37.8 + - + +
118A PHE 3.5 12.1 - - - -
119A LYS* 4.0 33.1 + - + -
130A ALA* 3.8 5.6 + - + +
131A HIS* 1.3 69.7 - - - +
133A GLU* 1.3 69.4 + - - +
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Residues in contact with GLU 133 (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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116A VAL 4.6 0.7 - - - -
117A GLU* 3.3 8.4 - - - +
118A PHE* 2.9 65.0 + - + -
131A HIS* 3.4 36.6 + - + +
132A HIS* 1.3 81.6 - - - +
134A LEU* 1.3 60.1 + - - +
135A SER* 4.0 5.3 + - - +
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Residues in contact with LEU 134 (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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115A GLN* 3.7 46.6 + - + +
116A VAL 3.7 6.7 - - - +
117A GLU* 3.9 27.4 - - + +
133A GLU* 1.3 73.1 + - - +
135A SER* 1.3 60.0 + - - +
136A THR* 4.2 2.4 + - - -
155A PRO* 6.2 0.5 - - - +
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Residues in contact with SER 135 (chain A).
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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56A MSE 2.6 39.9 - - - +
115A GLN* 3.2 7.6 - - - +
116A VAL 2.9 33.9 + - - -
118A PHE* 3.5 5.2 - - - -
133A GLU* 4.0 4.5 + - - +
134A LEU* 1.3 74.6 - - - +
136A THR* 1.3 62.3 + - - +
137A PHE* 3.5 11.3 - - - -
152A PHE* 3.7 16.2 - - - -
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Residues in contact with THR 136 (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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109A LEU* 4.2 9.0 - - + -
113A HIS* 4.2 3.1 - - + -
114A ALA 3.5 10.1 - - - +
115A GLN* 3.0 24.3 + - - +
134A LEU 4.2 2.3 + - - -
135A SER* 1.3 72.1 - - - +
137A PHE* 1.3 75.0 + - - +
152A PHE* 3.7 6.1 - - - -
153A LEU* 2.9 48.0 + - + +
182A TYR* 3.8 36.9 + - + +
183A ILE* 5.3 2.0 - - - -
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Residues in contact with PHE 137 (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* 3.7 23.3 - - + -
55A LEU* 3.8 21.3 - - + -
56A MSE 3.7 42.6 - - + -
59A ARG* 4.5 1.8 - - - -
113A HIS* 3.2 12.5 - - - +
114A ALA 2.9 33.1 + - - +
116A VAL* 3.6 17.9 - - + -
135A SER* 3.5 27.1 - - - -
136A THR* 1.3 75.3 - - - +
138A VAL* 1.3 60.5 + - - +
150A TRP* 3.8 17.9 - - + -
151A TYR 3.1 8.1 - - - +
152A PHE* 3.7 32.3 - + + -
153A LEU* 4.4 1.3 - - - +
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Residues in contact with VAL 138 (chain A).
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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76A LEU* 3.4 32.5 - - + -
112A ARG* 3.4 16.8 - - + +
113A HIS* 3.7 22.0 - - + +
137A PHE* 1.3 73.9 - - - +
139A LYS* 1.3 70.2 + - - +
140A ILE* 3.9 7.7 + - + -
149A SER 3.7 0.5 - - - +
150A TRP* 3.4 5.2 - - - -
151A TYR* 2.7 42.7 + - + +
153A LEU* 3.8 12.1 - - + +
169A CYS* 4.1 14.8 - - + -
179A CYS* 3.9 9.9 - - - -
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Residues in contact with LYS 139 (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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50A ASP 4.8 4.9 - - - -
112A ARG* 2.9 30.8 + - + +
138A VAL* 1.3 78.4 - - - +
140A ILE* 1.3 62.7 + - - +
148A ALA* 4.0 26.5 - - + -
149A SER 3.4 12.6 - - - +
150A TRP* 3.6 44.5 - - + +
169A CYS* 5.7 0.7 - - - -
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Residues in contact with ILE 140 (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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76A LEU* 3.5 31.9 - - + -
77A PRO* 3.8 13.7 - - + -
138A VAL* 4.1 8.7 - - + -
139A LYS* 1.3 77.9 - - - +
141A LYS* 1.3 77.1 + - - +
142A ASN 3.8 0.2 + - - -
148A ALA* 3.8 3.8 - - - -
149A SER* 2.9 28.8 + - - +
151A TYR* 3.6 29.8 - - + -
169A CYS* 3.7 28.3 - - + +
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Residues in contact with LYS 141 (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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139A LYS 4.5 0.2 + - - -
140A ILE* 1.3 89.1 - - - +
142A ASN* 1.3 71.4 + - - +
143A LYS* 3.8 1.0 + - - +
145A ASN 5.2 1.6 - - - +
146A SER* 4.6 10.3 - - - +
147A ASP 3.4 7.9 - - - +
148A ALA* 3.9 11.4 - - + -
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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