Contacts of the strand formed by residues 140 - 153 (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 GLU 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C LYS* 2.5 42.1 + - - -
8C ILE 4.7 0.3 - - - +
12C LYS* 3.9 16.7 + - - +
136C ASN* 2.4 28.6 + - - -
137C ILE 2.9 24.6 + - - +
138C SER 3.0 7.9 + - - +
139C ASN* 1.3 94.3 - - - +
141C TYR* 1.3 60.6 + - - +
142C TYR* 3.8 17.9 - - + +
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Residues in contact with TYR 141 (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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7C LYS* 3.7 3.8 - - - +
8C ILE* 2.8 50.0 + - + +
12C LYS* 3.6 26.5 - - - +
77C GLU* 2.9 36.6 + - + +
81C LYS* 3.2 20.1 - - - +
84C PHE* 3.8 23.3 - + + -
85C VAL* 3.7 25.8 - - + +
88C LEU* 5.3 0.4 - - + -
134C ILE* 4.0 15.5 - - + -
135C HIS 3.3 11.7 - - - -
136C ASN* 3.7 27.4 + - + -
139C ASN 5.2 1.8 - - - -
140C GLU* 1.3 77.6 + - - +
142C TYR* 1.3 59.9 + - - +
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Residues in contact with TYR 142 (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* 4.1 27.1 - - + -
6C TYR 3.2 8.1 - - - -
7C LYS* 3.6 40.4 - - + +
8C ILE* 3.6 8.8 - - - +
134C ILE* 3.5 6.1 - - - +
135C HIS* 2.7 34.9 + - + +
137C ILE* 3.6 49.7 + - + +
138C SER* 6.0 0.7 - - - -
140C GLU* 3.8 18.1 - - + +
141C TYR* 1.3 77.7 - - - +
143C LEU* 1.3 60.9 + - - +
254C TYR* 3.9 25.5 - + - -
255C GLN* 5.3 3.6 + - - -
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Residues in contact with LEU 143 (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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4C ASN 3.3 1.7 - - - +
5C LEU* 4.3 2.9 - - - -
6C TYR* 2.7 41.8 + - + +
8C ILE* 4.2 11.7 - - + -
92C ILE* 3.5 31.9 - - + -
132C ILE* 3.6 20.4 - - + -
133C LYS 3.4 13.7 - - - +
134C ILE* 3.7 11.9 - - + -
142C TYR* 1.3 73.3 - - - +
144C SER* 1.3 60.0 + - - +
145C ILE* 3.2 27.1 - - + +
244C LEU* 4.2 19.1 - - + -
247C ILE* 4.4 13.2 - - + -
248C THR* 5.0 8.5 - - + -
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Residues in contact with SER 144 (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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4C ASN* 3.1 22.7 - - - -
5C LEU* 3.9 8.1 - - - -
131C LYS 3.5 1.1 + - - +
132C ILE* 3.3 8.1 - - - +
133C LYS* 2.9 36.7 + - - +
135C HIS* 2.5 36.1 + - - -
143C LEU* 1.3 72.5 - - - +
145C ILE* 1.3 62.3 + - - +
146C LEU* 4.0 1.6 - - - -
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Residues in contact with ILE 145 (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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4C ASN* 3.2 22.2 + - - +
6C TYR* 3.4 25.8 - - + -
130C TYR* 3.5 28.0 - - + -
131C LYS 3.6 3.1 - - - -
132C ILE* 3.5 19.3 - - + -
143C LEU* 3.2 44.6 - - + +
144C SER* 1.3 73.6 - - - +
146C LEU* 1.3 58.5 + - - +
147C PRO* 3.3 9.5 - - - +
234C PHE* 4.2 1.0 - - - -
237C ILE* 3.6 19.2 - - + +
241C LEU* 3.7 15.9 - - + -
244C LEU* 4.9 3.1 - - + -
250C LEU* 5.1 4.3 - - + -
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Residues in contact with LEU 146 (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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4C ASN* 4.1 14.1 - - - +
130C TYR* 3.4 4.8 - - - -
131C LYS* 2.9 47.5 + - + +
144C SER* 5.7 0.7 - - - -
145C ILE* 1.3 72.3 - - - +
147C PRO* 1.3 79.9 - - + +
148C LYS* 3.5 22.3 + - + +
234C PHE* 4.3 13.5 - - + -
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Residues in contact with PRO 147 (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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128C LEU* 4.8 2.7 - - + -
129C THR 3.5 6.7 - - - +
130C TYR* 3.6 23.3 - - + -
145C ILE 3.3 11.4 - - - +
146C LEU* 1.3 94.8 - - + +
148C LYS* 1.3 62.7 + - - +
149C PHE* 6.5 0.4 - - + -
230C VAL* 4.0 17.8 - - + +
233C GLY* 3.8 16.4 - - - -
234C PHE* 3.5 52.5 - - + +
237C ILE* 4.7 0.9 - - + -
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Residues in contact with LYS 148 (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* 3.0 31.6 + - - +
128C LEU* 3.6 4.9 - - - +
129C THR* 2.8 49.0 + - + +
130C TYR 4.6 0.2 - - - +
131C LYS* 4.1 19.0 - - - +
146C LEU* 4.0 19.7 - - + +
147C PRO* 1.3 76.2 - - - +
149C PHE* 1.3 84.7 + - - +
150C THR* 5.1 1.6 - - - +
226C TYR* 4.5 16.6 - - + +
230C VAL* 5.1 1.6 - - - -
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Residues in contact with PHE 149 (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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116C PHE* 4.1 19.1 - + - -
126C ALA* 4.5 6.3 - - + -
127C HIS 3.4 21.3 - - - -
128C LEU* 3.9 29.2 - - + -
129C THR* 3.9 1.3 - - - -
148C LYS* 1.3 95.7 - - - +
150C THR* 1.3 63.1 + - - +
151C PHE* 4.0 24.0 + - + -
225C ILE* 3.6 31.4 - - + -
226C TYR* 3.2 24.5 + + + +
229C LYS* 3.4 35.9 - - + -
230C VAL* 4.0 15.3 - - + -
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Residues in contact with THR 150 (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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104C LYS* 4.7 12.9 + - + +
108C ASN* 5.8 0.5 - - - +
110C ILE* 3.8 24.4 - - + +
125C ASN 3.6 1.4 - - - +
126C ALA* 4.8 0.2 - - - -
127C HIS* 2.9 36.4 + - - +
129C THR* 2.7 31.5 + - - +
148C LYS* 5.1 1.4 - - - +
149C PHE* 1.3 74.6 + - - +
151C PHE* 1.3 64.5 + - - +
152C LEU* 3.9 17.0 - - + -
207C ASN* 3.6 20.6 - - - +
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Residues in contact with PHE 151 (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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118C LEU* 4.2 12.1 - - + -
124C VAL* 4.1 6.5 - - + -
125C ASN 3.3 4.9 - - - +
126C ALA* 3.7 31.2 - - + -
149C PHE* 4.0 21.1 - - + -
150C THR* 1.3 74.6 - - - +
152C LEU* 1.3 58.2 + - - +
207C ASN* 3.0 7.4 + - - +
208C PHE* 2.7 61.0 + - + +
209C THR* 5.6 3.6 - - - -
210C THR* 5.7 0.9 - - - -
218C PHE* 5.2 0.9 - + + -
222C VAL* 3.9 46.0 - - + -
225C ILE* 4.0 21.1 - - + -
226C TYR* 4.0 17.3 - + - -
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Residues in contact with LEU 152 (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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102C TYR* 4.9 2.7 - - + -
110C ILE* 4.3 12.6 - - + -
124C VAL* 3.6 1.9 - - - -
125C ASN* 2.8 32.9 + - - +
127C HIS* 3.9 29.8 - - + +
150C THR* 3.9 17.0 - - + -
151C PHE* 1.3 74.8 - - - +
153C SER* 1.3 69.6 + - - +
168C TYR* 4.0 33.4 - - + -
205C LEU* 4.2 16.4 - - + -
206C PHE 3.1 13.5 - - - +
207C ASN* 3.5 29.4 - - + +
208C PHE* 3.9 4.7 - - - -
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Residues in contact with SER 153 (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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123C ASN 3.7 6.5 - - - -
125C ASN* 4.8 0.9 - - - +
127C HIS* 5.6 0.3 + - - -
152C LEU* 1.3 76.5 - - - +
154C LYS* 1.3 65.1 + - - +
155C GLU 2.6 25.1 + - - -
160C SER* 3.6 20.0 - - - -
162C ILE* 4.8 0.2 - - - -
205C LEU* 3.5 15.8 - - - +
206C PHE* 2.7 47.9 + - - -
208C PHE* 3.5 8.8 - - - -
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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