Contacts of the strand formed by residues 120 - 131 (chain A) in PDB entry 5I2S
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 THR 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A THR 4.2 0.5 - - - +
67A THR* 4.2 0.2 - - - -
68A CYS 3.7 19.0 + - - -
113A SER* 2.8 39.4 + - - +
114A CYS* 3.7 1.2 - - - -
115A GLY* 3.4 20.3 + - - +
118A THR* 3.5 22.0 + - - +
119A VAL* 1.3 81.7 - - - +
121A ASP* 1.3 65.8 + - - +
122A ALA 4.1 0.9 + - - -
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Residues in contact with ASP 121 (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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65A VAL* 3.7 18.8 - - + +
66A THR 3.8 1.1 - - - -
67A THR* 3.0 35.3 + - - +
83A ARG* 4.8 12.1 + - - -
113A SER* 4.7 5.5 + - - -
119A VAL* 5.1 2.4 - - - +
120A THR* 1.3 74.9 - - - +
122A ALA* 1.3 61.9 + - - +
123A GLU* 4.3 4.9 - - + +
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Residues in contact with ALA 122 (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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65A VAL* 3.5 1.4 - - - -
66A THR* 2.8 40.7 + - - +
110A PRO* 3.2 12.4 - - + +
111A PRO* 3.5 24.7 - - + +
113A SER* 3.7 19.7 - - - +
120A THR 4.1 0.2 + - - -
121A ASP* 1.3 74.1 - - - +
123A GLU* 1.3 60.7 + - - +
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Residues in contact with GLU 123 (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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63A LYS* 3.2 41.9 + - - +
64A TRP 3.0 16.6 - - - +
65A VAL* 4.3 13.8 - - + +
110A PRO* 3.7 6.3 - - - +
121A ASP* 5.7 4.3 - - + -
122A ALA* 1.3 76.7 - - - +
124A ALA* 1.3 60.4 + - - +
125A VAL* 4.5 6.7 - - - +
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Residues in contact with ALA 124 (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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63A LYS* 3.8 1.0 - - - -
64A TRP* 2.9 33.0 + - - +
107A PRO* 4.7 21.8 - - + -
108A GLY 4.8 2.9 - - - +
110A PRO* 3.6 22.9 - - + +
123A GLU* 1.3 74.1 - - - +
125A VAL* 1.3 65.5 + - - +
126A ILE* 3.7 4.1 + - + +
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Residues in contact with VAL 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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62A SER 3.7 3.1 - - - -
63A LYS* 3.5 34.1 - - + -
85A PHE* 3.9 22.4 - - + -
91A GLN* 4.7 14.1 - - - +
107A PRO* 5.5 2.9 - - - +
123A GLU* 4.5 7.4 - - - +
124A ALA* 1.3 73.3 - - - +
126A ILE* 1.3 62.0 + - - +
127A VAL* 3.9 7.1 + - + +
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Residues in contact with ILE 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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60A HIS 4.2 0.2 - - - +
61A ALA* 3.5 1.4 - - - -
62A SER* 2.9 37.5 + - - +
64A TRP* 3.5 40.6 - - + +
104A TRP* 3.7 30.3 - - + -
106A ASN* 3.1 29.4 - - - +
107A PRO* 3.6 24.9 - - + -
108A GLY 4.0 8.1 - - - +
124A ALA 4.3 7.0 - - - +
125A VAL* 1.3 74.8 - - - +
127A VAL* 1.3 62.5 + - - +
128A GLN* 4.0 11.0 + - + +
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Residues in contact with VAL 127 (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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59A CYS* 3.8 24.9 - - - -
60A HIS 3.5 12.1 - - - +
61A ALA* 4.0 11.7 - - + -
85A PHE* 5.1 0.4 - - + -
87A PRO* 4.1 12.1 - - + -
91A GLN* 4.2 34.5 - - + +
95A SER* 2.5 39.1 + - - +
104A TRP* 3.1 14.1 + - - +
125A VAL* 3.9 11.6 + - + +
126A ILE* 1.3 77.2 - - - +
128A GLN* 1.3 57.9 + - - +
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Residues in contact with GLN 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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59A CYS* 3.4 3.3 - - - +
60A HIS* 2.9 74.2 + - + +
62A SER* 4.2 7.9 + - - -
64A TRP* 5.5 2.2 - - - -
104A TRP* 3.4 28.2 - - + -
106A ASN* 4.1 16.0 + - - +
126A ILE* 3.9 8.1 - - + +
127A VAL* 1.3 73.8 - - - +
129A VAL* 1.3 63.3 + - - +
130A THR* 4.2 5.8 - - + +
408A PRO 5.1 1.2 - - - +
409A HIS* 3.6 24.1 - - - +
412A ASP* 4.2 14.9 - - - +
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Residues in contact with VAL 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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57A TRP* 4.1 15.8 - - + -
58A MET 3.2 5.6 - - - +
59A CYS* 3.6 24.7 - - + -
92A CYS 4.0 0.2 - - - +
95A SER* 3.5 26.2 - - - +
96A ILE* 3.6 30.7 - - + +
99A THR* 3.2 36.4 - - - +
104A TRP* 5.2 1.2 - - - +
128A GLN* 1.3 81.4 - - - +
130A THR* 1.3 65.2 + - - +
131A PRO* 4.4 1.7 - - - +
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Residues in contact with THR 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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57A TRP* 3.5 3.4 - - - -
58A MET* 2.9 39.5 + - - +
60A HIS* 4.2 21.0 - - + -
128A GLN* 5.0 5.2 - - + +
129A VAL* 1.3 80.6 - - - +
131A PRO* 1.3 77.4 + - + +
132A HIS* 4.0 0.7 - - - +
408A PRO* 6.3 0.2 - - + -
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Residues in contact with PRO 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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15A LYS* 4.6 7.6 - - - +
56A GLY 3.4 9.0 - - - +
57A TRP* 3.5 27.8 - - + -
99A THR* 6.1 0.7 - - + -
129A VAL 4.4 1.1 - - - +
130A THR* 1.3 90.6 + - - +
132A HIS* 1.3 62.9 + - - +
133A HIS* 5.1 10.8 - - - +
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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