Contacts of the strand formed by residues 124 - 137 (chain A) in PDB entry 5I4A
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 VAL 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A SER* 3.5 7.0 + - - -
118A LEU* 3.1 54.1 + - + -
121A ASN* 3.3 26.4 + - + +
122A GLU 3.3 1.2 - - - -
123A ASN* 1.3 82.4 - - - +
125A ASN* 1.3 72.1 + - - +
151A PHE* 4.1 10.1 - - + -
152A LEU 3.7 8.3 - - - +
162A ILE* 4.0 10.8 - - + -
208A PHE* 4.0 27.8 - - + -
218A PHE* 4.2 10.5 - - + -
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Residues in contact with ASN 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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115A VAL* 3.7 16.8 - - + +
116A PHE 3.9 0.4 - - - -
117A SER* 3.7 29.5 - - - +
123A ASN 4.3 0.2 + - - -
124A VAL* 1.3 75.0 + - - +
126A ALA* 1.3 59.0 + - - +
127A HIS* 3.3 25.3 + - + +
150A THR 3.6 1.6 - - - +
151A PHE* 3.2 6.2 - - - +
152A LEU 2.6 39.3 + - - +
153A SER 4.6 0.2 - - - +
154A LYS* 3.2 38.8 - - - +
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Residues in contact with ALA 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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114A GLU 3.8 0.9 - - - +
115A VAL* 3.5 4.0 - - - -
116A PHE* 2.9 67.0 + - + +
118A LEU* 4.3 6.4 - - + +
124A VAL 4.1 0.4 + - - -
125A ASN* 1.3 69.0 - - - +
127A HIS* 1.3 63.6 + - - +
128A LEU 3.7 1.4 + - - -
149A PHE* 4.4 5.4 - - + -
150A THR 3.7 4.0 - - - -
151A PHE* 3.7 27.4 - - + -
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Residues in contact with HIS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 5.6 2.9 - + - -
110A ILE* 3.4 26.5 - - + +
111A SER 3.1 18.7 + - - +
112A ASN* 4.0 14.1 + - - -
114A GLU 3.9 4.0 - - - -
115A VAL* 3.3 22.0 - - + +
125A ASN* 3.3 35.4 + - + +
126A ALA* 1.3 71.0 - - - +
128A LEU* 1.3 65.0 + - - +
129A THR* 3.0 1.8 + - - +
149A PHE* 3.5 4.4 - - - -
150A THR* 2.7 41.8 + - - +
152A LEU* 3.8 26.2 - - + +
153A SER 5.4 1.2 + - - -
205A LEU* 5.5 3.6 - - + +
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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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109A PHE 4.2 0.2 - - - +
111A SER* 2.9 33.4 + - - -
114A GLU* 3.0 46.7 + - + +
126A ALA 3.7 1.6 + - - -
127A HIS* 1.3 71.1 - - - +
129A THR* 1.3 70.5 + - - +
130A TYR* 4.0 35.2 - - + +
147A PRO* 4.9 0.7 - - + -
148A LYS 3.7 14.4 - - - +
149A PHE* 4.0 23.7 - - + -
229A LYS 5.8 0.2 - - - +
233A GLY* 4.6 12.8 - - - -
236A LYS* 4.1 19.5 - - + +
240A THR* 4.8 2.7 - - + -
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Residues in contact with THR 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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108A ASN* 4.2 11.9 - - + -
109A PHE 3.3 26.9 - - - +
110A ILE* 3.9 8.7 - - + +
127A HIS 3.0 11.6 + - - -
128A LEU* 1.3 75.6 + - - +
130A TYR* 1.3 67.6 + - - +
147A PRO* 3.5 4.0 - - - +
148A LYS* 2.7 58.5 + - + +
150A THR* 2.4 31.6 + - - +
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Residues in contact with TYR 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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96A PHE* 4.7 6.1 - - + -
101A PHE* 4.6 9.6 - + - -
107A ASN 3.8 1.2 - - - +
108A ASN* 3.7 0.2 - - - -
109A PHE* 2.8 43.2 + - - +
128A LEU* 4.0 24.1 - - + +
129A THR* 1.3 78.0 - - - +
131A LYS* 1.3 57.5 + - - +
132A ILE* 4.2 13.9 - - + -
145A ILE* 3.5 18.4 - - + -
146A LEU 3.5 1.3 - - - -
147A PRO* 3.7 23.1 - - + -
233A GLY* 2.7 34.8 + - - -
236A LYS* 3.8 15.6 + - - +
237A ILE* 3.6 18.8 + - + -
240A THR* 4.1 12.7 - - + -
241A LEU* 3.8 28.9 - - + -
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Residues in contact with LYS 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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106A GLY 3.3 19.3 - - - +
107A ASN 3.5 4.5 - - - +
108A ASN* 3.2 25.8 + - - +
129A THR* 4.3 0.6 - - - +
130A TYR* 1.3 72.4 - - - +
132A ILE* 1.3 64.9 + - - +
133A LYS* 3.8 16.8 - - - +
144A SER 3.5 0.7 - - - +
146A LEU* 2.9 35.7 + - + +
148A LYS* 3.8 15.4 - - - +
545A ASN* 5.2 7.3 + - - +
547A ASN* 2.9 32.6 + - - +
9B C 2.8 30.4 + - - +
10B U 3.0 22.0 + - - -
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Residues in contact with ILE 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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89A TYR* 4.1 3.7 - - + -
92A ILE* 4.2 12.8 - - + -
96A PHE* 3.8 20.9 - - + -
107A ASN* 3.1 30.0 + - + +
109A PHE* 3.8 30.3 - - + -
130A TYR* 4.1 5.4 - - + +
131A LYS* 1.3 82.4 - - - +
133A LYS* 1.3 70.1 + - - +
143A LEU* 3.5 36.6 - - + -
144A SER 3.3 2.0 - - - +
145A ILE* 3.7 35.7 - - + -
244A LEU* 5.0 1.1 - - + -
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Residues in contact with LYS 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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89A TYR* 3.4 13.2 - - - +
106A GLY* 3.8 21.9 + - - -
107A ASN* 3.8 11.1 - - - +
131A LYS* 3.8 5.6 - - - +
132A ILE* 1.3 79.7 - - - +
134A ILE* 1.3 64.1 + - - +
135A HIS* 3.5 11.9 - - + +
143A LEU* 3.4 7.3 - - - +
144A SER* 2.9 44.9 + - - +
545A ASN 6.0 1.6 - - - +
547A ASN* 3.7 21.3 - - + -
9B C 4.7 1.0 + - - -
10B U 3.4 34.6 + - - -
11B A 2.8 22.9 + - - +
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Residues in contact with ILE 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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8A ILE* 4.7 0.7 - - + -
85A VAL* 3.9 14.7 - - + +
88A LEU* 3.8 26.5 - - + -
89A TYR* 2.8 69.6 + - + +
92A ILE* 4.1 3.4 - - + -
133A LYS* 1.3 70.6 - - - +
135A HIS* 1.3 71.1 + - - +
141A TYR* 4.0 24.5 - - + -
142A TYR 3.4 9.2 - - - +
143A LEU* 3.7 19.3 - - + -
11B A 4.5 5.7 + - - -
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Residues in contact with HIS 135 (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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5A LEU* 3.7 9.4 - - + -
133A LYS* 3.5 23.7 - - + +
134A ILE* 1.3 79.1 + - - +
136A ASN* 1.3 60.1 + - - +
137A ILE* 3.8 22.1 + - + -
140A GLU 3.7 0.9 - - - +
141A TYR* 3.4 4.2 - - - -
142A TYR* 2.7 41.6 + - + +
144A SER* 2.4 44.3 + - - -
543A ASN* 6.4 0.2 - - - -
546A THR* 5.8 0.4 - - - -
547A ASN* 4.6 7.0 - - + -
548A ILE* 3.7 25.4 - - + +
580A GLU* 4.1 13.7 + - - -
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Residues in contact with ASN 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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81A LYS* 2.8 29.1 + - - +
135A HIS* 1.3 70.2 - - - +
137A ILE* 1.3 60.8 + - - +
138A SER 4.2 0.6 + - - -
139A ASN* 4.0 10.0 - - - +
140A GLU 3.0 29.3 + - - +
141A TYR* 3.7 29.2 - - + -
562A ASP* 4.0 5.9 - - - +
565A THR* 5.3 1.6 + - - +
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Residues in contact with ILE 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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5A LEU* 3.7 29.6 - - + -
135A HIS* 3.8 19.2 + - + -
136A ASN* 1.3 76.7 - - - +
138A SER* 1.3 72.9 + - - +
139A ASN 3.3 1.3 - - - -
140A GLU* 2.9 18.5 + - - +
142A TYR* 3.4 28.9 - - + -
254A TYR* 4.6 7.6 - - + +
548A ILE* 4.6 0.2 - - + -
561A LEU* 3.4 54.5 - - + +
562A ASP* 3.4 15.0 - - + +
565A THR* 6.1 1.6 - - + -
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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