Contacts of the strand formed by residues 104 - 117 (chain U) in PDB entry 5C3I
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 GLN 104 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100U THR* 3.2 3.3 - - - -
101U TYR 3.0 32.6 + - - +
102U ARG* 3.6 35.0 + - - +
103U GLY* 1.3 78.0 - - - +
105U GLU* 1.3 63.3 + - - +
106U PHE 3.5 1.4 + - - -
151U ILE* 3.6 22.1 - - + +
152U ASN* 3.4 43.8 + - - +
118X ARG* 5.1 8.1 + - - +
122X ARG* 3.7 26.2 + - - +
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Residues in contact with GLU 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98U THR* 3.3 13.8 - - - +
99U CYS 3.6 8.3 - - - +
100U THR* 3.5 22.4 - - + +
103U GLY 4.0 2.0 + - - -
104U GLN* 1.3 69.0 - - - +
106U PHE* 1.3 60.9 + - - +
107U ILE 4.1 9.0 - - - +
108U ARG* 2.7 41.9 + - - +
149U PHE* 3.7 25.7 - - - +
151U ILE* 3.4 12.4 - - - +
134V ARG* 2.9 38.1 + - - +
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Residues in contact with PHE 106 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4U VAL* 3.7 43.7 - - + -
6U VAL* 5.2 3.8 - - + -
38U LEU* 3.9 15.0 - - + -
40U TRP* 5.5 1.3 - + - -
99U CYS* 3.1 55.9 + - + -
100U THR 3.9 2.5 - - - -
101U TYR* 4.0 12.6 - - + -
104U GLN 4.0 1.1 - - - -
105U GLU* 1.3 74.8 - - - +
107U ILE* 1.3 77.5 + - + +
148U ARG* 3.3 6.8 - - - +
149U PHE* 2.8 39.9 + - - +
151U ILE* 3.8 27.4 - - + -
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Residues in contact with ILE 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6U VAL* 3.8 35.9 - - + +
40U TRP* 5.3 1.6 - - + -
97U ILE 5.3 1.3 - - - +
98U THR* 3.3 7.9 - - - -
99U CYS* 3.2 42.2 + - + +
105U GLU* 3.9 4.2 - - - +
106U PHE* 1.3 105.3 - - + +
108U ARG* 1.3 64.0 + - - +
109U VAL* 4.1 12.3 - - + -
146U VAL* 3.6 28.0 - - + -
147U THR 3.5 8.5 - - - +
148U ARG* 4.3 18.4 - - + +
149U PHE* 5.2 0.2 - - - -
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Residues in contact with ARG 108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43U ILE* 4.4 13.5 - - - +
96U LEU* 4.2 33.9 - - + +
97U ILE 3.6 3.6 - - - -
98U THR* 3.3 18.9 + - + +
105U GLU* 2.7 35.3 + - - +
107U ILE* 1.3 76.1 - - - +
109U VAL* 1.3 62.9 + - - +
110U GLY 4.0 0.6 + - - +
145U ARG 3.7 3.3 - - - +
147U THR* 2.9 40.2 + - - +
149U PHE* 4.4 8.3 - - + -
129V ARG* 4.8 5.3 + - - +
130V ILE 5.2 1.3 - - - +
132V GLY* 3.3 36.9 + - - -
133V GLU 4.8 0.8 + - - -
134V ARG* 3.5 37.9 - - - +
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Residues in contact with VAL 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6U VAL* 5.4 2.0 - - + -
9U VAL* 5.0 9.0 - - + -
95U VAL 3.7 0.7 - - - +
96U LEU* 3.3 5.5 - - - -
97U ILE* 2.8 53.5 + - + +
107U ILE* 4.1 25.1 - - + -
108U ARG* 1.3 75.3 - - - +
110U GLY* 1.3 60.7 + - - +
111U TYR* 3.8 28.2 - - + +
144U PRO* 4.3 14.8 - - + -
145U ARG 3.9 3.1 - - - +
146U VAL* 4.2 18.4 - - + -
100W PHE* 4.6 11.4 - - + -
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Residues in contact with GLY 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95U VAL 3.4 6.7 - - - -
96U LEU* 3.8 11.8 - - - +
108U ARG 4.0 1.2 + - - -
109U VAL* 1.3 73.6 - - - +
111U TYR* 1.3 61.4 + - - -
144U PRO* 3.5 6.4 - - - +
145U ARG 3.2 32.7 + - - -
130V ILE* 3.5 28.4 + - - +
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Residues in contact with TYR 111 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U VAL* 3.4 35.4 + - + +
11U VAL* 4.3 9.4 - - + +
24U PHE* 4.3 10.8 - + + -
94U VAL* 3.3 7.8 - - - +
95U VAL* 2.9 38.6 + - + +
97U ILE* 4.0 22.7 - - + -
109U VAL* 3.8 23.1 - - + +
110U GLY* 1.3 77.0 - - - -
112U TYR* 1.3 60.6 + - - +
113U VAL* 4.1 3.8 - - + +
139U ILE* 3.8 21.5 - - + -
140U LEU 3.5 17.5 - - - -
141U ALA* 3.7 24.8 + - - -
144U PRO* 3.7 29.3 - - + +
130V ILE* 3.6 4.9 - - - +
100W PHE* 5.1 1.0 - - - -
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Residues in contact with TYR 112 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92U VAL* 4.0 22.0 - - + -
93U THR 3.7 1.6 - - - -
94U VAL* 3.7 20.6 - - + -
111U TYR* 1.3 73.1 - - - +
113U VAL* 1.3 56.4 + - - +
114U ASN 4.2 0.7 - - - -
138U ASN 3.9 0.4 - - - +
139U ILE* 3.5 2.1 - - - +
140U LEU* 2.6 66.9 + - + +
143U ASN 5.2 2.2 + - - -
145U ARG* 5.5 0.4 - - + -
106V ASP* 3.4 25.2 + - - +
109V LEU* 4.3 15.3 - - + -
110V CYS* 3.5 32.3 - - + +
113V HIS* 4.8 4.0 - + + -
126V LEU* 4.4 7.0 - - + -
127V ALA* 3.4 26.9 - - - +
130V ILE* 3.4 30.7 - - + +
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Residues in contact with VAL 113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44U TYR* 5.1 3.4 - - + -
92U VAL* 3.4 3.0 - - - +
93U THR* 2.7 51.3 + - + +
95U VAL* 3.4 34.8 - - + -
111U TYR 4.1 6.1 - - - +
112U TYR* 1.3 78.3 - - - +
114U ASN* 1.3 60.7 + - - +
115U ASN* 3.7 5.5 + - - +
137U ARG* 3.9 31.9 - - + -
138U ASN 3.6 3.8 - - - +
139U ILE* 3.8 29.6 - - + -
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Residues in contact with ASN 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91U GLY* 3.8 1.6 - - - -
92U VAL* 3.6 21.5 + - + +
113U VAL* 1.3 71.1 - - - +
115U ASN* 1.3 76.8 + - - +
116U GLU* 3.6 25.1 + - - +
136U GLN 3.7 0.9 - - - +
137U ARG* 3.3 4.9 - - - -
138U ASN* 2.8 45.7 + - + +
113V HIS* 3.6 39.0 + - + +
114V ALA* 5.0 3.5 - - - +
115V LYS* 5.1 6.7 - - - +
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Residues in contact with ASN 115 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18U PHE* 3.6 27.7 - - - -
44U TYR* 3.4 19.8 + - - -
88U ASP 4.7 1.0 + - - -
89U ALA 2.9 27.5 + - - +
90U VAL* 4.2 6.0 - - - +
91U GLY* 3.0 35.7 + - - +
93U THR* 3.8 11.7 - - - +
113U VAL* 4.6 3.4 - - - +
114U ASN* 1.3 81.1 + - - +
116U GLU* 1.3 65.3 + - - +
135U LEU* 4.5 10.7 - - + +
136U GLN 3.8 3.3 - - - +
137U ARG* 3.9 12.1 - - - +
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Residues in contact with GLU 116 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90U VAL* 4.7 4.0 - - - -
114U ASN* 3.6 19.4 + - - +
115U ASN* 1.3 77.5 - - - +
117U TYR* 1.3 73.3 + - - +
118U THR 3.8 0.2 + - - -
123U ARG* 3.2 32.5 + - - -
135U LEU* 3.5 10.4 - - - +
136U GLN* 2.8 46.7 + - + +
115V LYS* 4.0 19.0 + - - -
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Residues in contact with TYR 117 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90U VAL* 3.7 26.9 - - + +
116U GLU* 1.3 80.7 - - - +
118U THR* 1.3 52.4 - - - +
119U GLU 3.2 3.4 - - - +
122U LEU* 4.0 38.1 - - + -
123U ARG* 2.2 43.2 + - + +
126U PRO* 5.2 4.3 - - + -
127U PRO* 3.7 27.5 + - + +
130U PRO* 3.5 10.2 - - - +
131U ASP* 2.9 51.2 + - + -
134U LYS* 3.6 21.1 - - + -
135U LEU* 3.5 15.4 - - + +
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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
------------------------------------------------------------
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