Contacts of the strand formed by residues 124 - 137 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C SER* 3.5 4.6 + - - -
118C LEU* 3.0 50.1 + - + +
121C ASN* 3.1 15.1 + - + +
122C GLU 3.2 0.2 - - - -
123C ASN* 1.3 84.1 - - - +
125C ASN* 1.3 72.3 + - - +
151C PHE* 4.1 10.3 - - + -
152C LEU 3.6 9.6 - - - +
162C ILE* 3.8 28.5 - - + -
208C PHE* 3.8 21.3 - - + -
218C PHE* 4.1 13.7 - - + -
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Residues in contact with ASN 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C VAL* 3.8 11.7 - - + +
116C PHE 3.8 2.2 - - - -
117C SER* 3.5 25.3 - - - +
118C LEU* 5.1 0.2 - - - -
123C ASN 4.2 0.2 + - - -
124C VAL* 1.3 76.0 - - - +
126C ALA* 1.3 60.0 + - - +
127C HIS* 3.5 24.7 + - - +
150C THR 3.6 1.2 - - - +
151C PHE* 3.3 6.8 - - - -
152C LEU 2.8 36.7 + - - +
153C SER 4.8 0.3 - - - +
154C LYS* 3.1 44.5 - - - +
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLU 3.8 1.0 - - - +
115C VAL* 3.2 5.6 - - - -
116C PHE* 2.9 67.6 + - + +
118C LEU* 4.0 5.6 - - + +
124C VAL 4.2 0.2 + - - -
125C ASN* 1.3 71.8 - - - +
127C HIS* 1.3 60.9 + - - +
128C LEU 3.9 0.3 + - - -
149C PHE* 4.5 5.2 - - + -
150C THR 3.8 3.8 - - - -
151C PHE* 3.7 25.8 - - + -
225C ILE* 4.4 0.2 - - + -
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Residues in contact with HIS 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TYR* 5.4 2.7 - + - -
110C ILE* 3.4 26.5 - - + +
111C SER 3.0 19.8 + - - +
112C ASN* 3.8 17.6 + - - -
114C GLU 3.7 4.3 - - - -
115C VAL* 3.4 21.0 - - + +
125C ASN* 3.5 29.0 + - + +
126C ALA* 1.3 71.0 - - - +
128C LEU* 1.3 64.6 + - - +
129C THR* 3.1 1.6 + - - +
149C PHE* 3.4 6.5 - - - -
150C THR 2.9 41.5 + - - +
152C LEU* 3.9 26.8 - - + +
153C SER 5.6 0.6 + - - -
205C LEU* 5.7 3.0 - - + +
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Residues in contact with LEU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C PHE 4.1 0.2 - - - +
111C SER* 2.9 31.4 + - - -
114C GLU* 2.9 44.2 + - + +
126C ALA 3.9 0.6 + - - -
127C HIS* 1.3 70.4 - - - +
129C THR* 1.3 69.3 + - - +
130C TYR* 3.6 37.7 - - + +
147C PRO* 4.8 1.3 - - + -
148C LYS 3.6 13.2 - - - +
149C PHE* 3.9 26.1 - - + -
229C LYS 5.4 0.2 - - - +
233C GLY* 4.5 13.7 - - - -
236C LYS* 4.5 18.2 - - + -
240C THR* 4.8 2.2 - - + -
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Residues in contact with THR 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ASN* 4.0 13.9 - - + -
109C PHE 3.3 26.5 - - - +
110C ILE* 3.8 8.3 - - + +
127C HIS 3.1 11.3 + - - -
128C LEU* 1.3 75.2 + - - +
130C TYR* 1.3 68.8 + - - +
147C PRO* 3.5 4.0 - - - +
148C LYS* 2.8 56.1 + - + +
150C THR* 2.7 31.0 + - - +
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Residues in contact with TYR 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C PHE* 4.8 5.2 - - + -
101C PHE* 4.6 9.2 - + - -
107C ASN 3.5 2.3 - - - +
109C PHE* 2.8 39.9 + - - +
111C SER* 6.0 0.2 - - - -
128C LEU* 3.6 36.7 - - + +
129C THR* 1.3 76.9 - - - +
131C LYS* 1.3 60.2 + - - +
132C ILE* 4.2 15.3 - - + -
145C ILE* 3.5 18.2 - - + -
146C LEU 3.4 1.8 - - - -
147C PRO* 3.6 29.8 - - + -
233C GLY* 2.7 26.4 + - - -
236C LYS* 3.8 10.6 + - - +
237C ILE* 3.7 16.9 + - + -
240C THR* 4.4 7.4 - - + -
241C LEU* 3.9 29.8 - - + -
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLY* 3.4 32.7 + - - +
107C ASN 3.4 3.6 - - - -
108C ASN* 3.2 26.6 + - - +
129C THR 4.3 0.4 - - - -
130C TYR* 1.3 72.4 - - - +
132C ILE* 1.3 61.4 + - - +
133C LYS* 3.6 25.4 + - + +
144C SER* 3.5 4.0 + - - +
145C ILE* 3.6 1.4 - - - -
146C LEU* 2.9 48.0 + - + +
148C LYS* 4.1 19.5 - - - +
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Residues in contact with ILE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C TYR* 4.2 2.6 - - + -
92C ILE* 4.0 15.0 - - + -
96C PHE* 3.8 19.3 - - + -
107C ASN* 3.0 32.6 + - + +
109C PHE* 3.6 33.4 - - + -
130C TYR* 4.0 7.0 - - + +
131C LYS* 1.3 81.1 - - - +
133C LYS* 1.3 71.4 + - - +
143C LEU* 3.6 33.9 - - + -
144C SER 3.3 2.0 - - - +
145C ILE* 3.5 33.9 - - + -
241C LEU* 4.7 0.7 - - + -
244C LEU* 5.1 1.3 - - + -
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Residues in contact with LYS 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C TYR* 3.6 16.0 + - - +
106C GLY* 3.6 27.5 + - - -
107C ASN* 3.9 12.7 - - - +
131C LYS* 3.6 22.9 - - + +
132C ILE* 1.3 83.4 - - - +
134C ILE* 1.3 65.6 + - - +
135C HIS* 3.6 12.6 - - + +
143C LEU* 3.4 7.9 - - - +
144C SER* 2.9 44.9 + - - +
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Residues in contact with ILE 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 4.6 5.4 - - + -
85C VAL* 4.0 14.9 - - + +
88C LEU* 3.8 22.4 - - + -
89C TYR* 3.0 69.6 + - + +
92C ILE* 3.8 3.6 - - + -
133C LYS* 1.3 74.0 - - - +
135C HIS* 1.3 70.8 + - - +
141C TYR* 4.0 23.6 - - + -
142C TYR 3.5 8.5 - - - +
143C LEU* 3.7 15.9 - - + -
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Residues in contact with HIS 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.8 13.2 - - + +
133C LYS* 3.6 19.2 - - + +
134C ILE* 1.3 79.8 + - - +
136C ASN* 1.3 60.0 + - - +
137C ILE* 3.8 22.9 + - + -
141C TYR* 3.3 7.6 - - - -
142C TYR* 2.7 39.6 + - + +
144C SER* 2.5 44.0 + - - -
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Residues in contact with ASN 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LYS* 3.5 27.7 + - - +
135C HIS* 1.3 70.2 - - - +
137C ILE* 1.3 62.0 + - - +
138C SER 4.2 1.4 + - - -
139C ASN* 3.9 9.5 + - - +
140C GLU 2.4 42.6 + - - +
141C TYR* 3.7 29.0 + - + -
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Residues in contact with ILE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.7 30.7 - - + -
135C HIS* 3.8 21.9 + - + -
136C ASN* 1.3 76.9 - - - +
138C SER* 1.3 80.1 + - - +
139C ASN 3.3 1.1 - - - -
140C GLU* 2.9 23.2 + - - +
142C TYR* 3.6 24.7 + - + -
254C TYR* 4.6 14.6 - - + +
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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