Contacts of the strand formed by residues 99 - 109 (chain B) in PDB entry 5IXG
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 LYS 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B ARG* 3.2 28.8 - - - +
95B PHE* 3.3 4.5 - - - -
96B ASP 3.0 29.1 + - - +
97B GLY 3.3 1.0 - - - -
98B ASP* 1.3 108.3 + - - +
100B PRO* 1.3 75.2 - - + +
101B VAL* 3.4 3.3 - - + +
123B PHE* 3.5 37.5 - - + +
124B LYS* 6.3 0.4 - - - +
160C LYS* 5.5 7.2 - - - +
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Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 4.4 7.2 - - + -
46B ARG* 5.7 0.4 - - - +
93B ILE* 3.7 19.5 - - + -
94B LYS 3.5 8.3 - - - +
95B PHE* 3.5 26.4 - - + -
99B LYS* 1.3 94.5 - - + +
101B VAL* 1.4 61.5 + - - +
120B ILE* 3.8 26.1 - - + +
123B PHE* 3.8 43.8 - - + +
201B OTP 6.1 0.4 - - + -
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 2.8 16.7 + - + +
95B PHE 3.9 2.7 - - - +
96B ASP* 3.5 39.3 - - + +
99B LYS* 3.4 13.9 - - + +
100B PRO* 1.4 80.1 - - - +
102B SER* 1.4 71.4 + - - +
119B LYS* 3.7 7.3 - - - +
120B ILE* 2.9 32.6 + - - +
160C LYS* 5.2 8.3 - - + -
162C LYS* 6.3 3.4 - - + -
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 3.4 7.1 - - - +
94B LYS* 2.9 47.1 + - - +
101B VAL* 1.4 83.8 - - - +
103B VAL* 1.3 67.9 + - - +
104B VAL* 4.2 4.3 - - - +
117B THR* 4.4 13.2 - - - -
118B LEU 3.1 13.9 - - - -
119B LYS* 4.5 2.0 - - - -
120B ILE* 3.9 4.5 - - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 4.2 9.4 - - + -
89B TYR* 3.1 27.0 + - + +
91B GLY 3.6 19.7 - - - +
92B THR 3.3 13.7 - - - +
93B ILE* 4.2 7.4 - - + +
102B SER* 1.3 80.3 - - - +
104B VAL* 1.3 64.4 + - - +
117B THR* 3.2 4.2 - - - +
118B LEU* 2.8 37.8 + - + +
120B ILE* 4.1 11.2 - - + -
201B OTP 3.9 34.3 - - + -
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B TYR* 3.8 0.9 - - - -
91B GLY* 3.3 0.3 - - - -
92B THR* 2.9 34.1 + - - +
94B LYS* 4.1 30.3 - - + -
102B SER* 4.2 4.0 - - - +
103B VAL* 1.3 77.4 - - - +
105B GLY* 1.3 62.1 + - - +
117B THR* 4.0 25.8 - - + +
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Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B TYR* 3.4 3.0 + - - -
90B LYS 3.2 13.9 - - - -
91B GLY* 3.7 2.0 - - - -
104B VAL* 1.3 79.5 - - - +
106B ASN* 1.3 74.2 + - - -
115B PRO* 3.4 5.5 - - - +
116B LEU 2.9 32.5 + - - -
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Residues in contact with ASN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ASN* 3.8 1.2 - - - +
89B TYR* 3.4 9.2 - - - -
90B LYS* 2.9 33.9 + - + +
105B GLY* 1.3 84.0 + - - -
107B LEU* 1.3 58.9 + - - +
108B THR* 5.2 0.9 + - - -
113B THR* 3.8 20.7 - - + +
114B LYS* 3.4 6.3 + - - +
115B PRO* 3.6 24.2 - - - +
116B LEU 4.2 0.7 - - - +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ALA* 4.4 2.0 - - + -
88B ASN 3.5 15.9 - - - +
89B TYR* 3.9 6.0 - - + -
106B ASN* 1.3 73.3 - - - +
108B THR* 1.3 69.3 + - - +
109B LEU* 4.0 22.9 - - + -
112B VAL 3.4 2.4 - - - +
113B THR* 3.3 2.2 - - - -
114B LYS 2.9 30.8 + - - +
116B LEU* 3.9 29.6 - - + +
144B PHE* 4.7 8.5 - - + -
149B PHE* 3.4 26.6 - - + -
201B OTP 3.9 43.3 - - + -
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLN 4.4 3.1 - - - +
87B ALA* 3.2 8.3 - - - +
88B ASN* 2.8 48.6 + - + -
106B ASN* 5.2 0.9 + - - +
107B LEU* 1.3 70.1 - - - +
109B LEU* 1.3 62.0 + - - +
111B GLY* 4.1 20.0 - - - +
112B VAL 3.2 6.7 - - - +
113B THR* 2.7 29.2 + - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 4.1 12.1 - - + -
79B PHE* 4.1 13.2 - - + -
86B GLN 5.1 0.9 - - - -
87B ALA* 4.0 10.8 - - + +
107B LEU* 4.0 15.0 - - + -
108B THR* 1.3 76.3 - - - +
110B HIS* 1.3 76.9 + - - +
111B GLY 3.1 0.4 - - - -
112B VAL* 3.0 18.7 + - - +
144B PHE* 4.0 25.8 - - + -
149B PHE* 3.6 29.9 - - + +
151B LEU* 3.9 22.7 - - + -
201B OTP 3.9 31.0 - - + -
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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