Contacts of the strand formed by residues 99 - 109 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A LYS* 5.7 7.4 - - + +
46D ARG* 6.2 0.4 - - - +
95D PHE* 3.2 5.6 - - - -
96D ASP 2.9 31.1 + - - +
97D GLY 3.2 1.8 - - - -
98D ASP* 1.3 88.3 - - + +
100D PRO* 1.3 77.5 - - + +
101D VAL* 3.4 4.8 - - + +
123D PHE* 3.2 43.0 + - + +
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Residues in contact with PRO 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 4.5 5.2 - - + -
46D ARG* 5.0 3.4 - - + -
93D ILE* 3.7 20.4 - - + -
94D LYS 3.5 7.4 - - - +
95D PHE* 3.6 25.7 - - + -
98D ASP 4.2 0.7 - - - +
99D LYS* 1.3 99.4 - - + +
101D VAL* 1.3 63.7 + - - +
120D ILE* 3.8 26.5 - - + +
123D PHE* 4.0 38.5 - - + +
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LYS* 5.5 6.1 - - + +
162A LYS* 6.3 4.9 - - + -
94D LYS* 2.8 18.0 + - + +
95D PHE 3.9 3.1 - - - +
96D ASP* 3.6 39.5 - - + +
99D LYS* 3.4 14.8 - - + +
100D PRO* 1.3 80.2 - - - +
102D SER* 1.3 71.2 + - - +
119D LYS* 3.8 6.6 - - - +
120D ILE* 2.8 32.0 + - - +
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Residues in contact with SER 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE* 3.4 7.4 - - - +
94D LYS* 2.9 46.4 + - - +
101D VAL* 1.3 86.5 - - - +
103D VAL* 1.3 65.3 + - - +
104D VAL* 3.9 6.4 - - - +
117D THR* 4.1 14.5 - - - +
118D LEU 3.2 14.1 - - - -
119D LYS* 4.3 2.7 - - - -
120D ILE* 3.8 6.1 - - - +
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D VAL* 4.1 13.7 - - + -
89D TYR* 3.1 31.4 + - + +
91D GLY 3.8 16.2 - - - -
92D THR 3.3 12.8 - - - +
93D ILE* 4.4 4.5 - - + -
102D SER* 1.3 78.1 - - - +
104D VAL* 1.3 64.0 + - - +
117D THR* 3.1 5.0 - - - +
118D LEU* 2.8 37.9 + - + +
120D ILE* 4.1 11.0 - - + -
201D OTP 3.9 35.0 - - + -
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Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D TYR* 3.9 0.7 - - - -
91D GLY* 3.3 0.5 - - - -
92D THR* 2.8 35.6 + - - +
94D LYS* 3.7 45.3 - - + +
102D SER* 3.9 8.1 - - - +
103D VAL* 1.3 74.3 - - - +
105D GLY* 1.3 62.2 + - - +
117D THR* 4.1 21.5 - - + +
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Residues in contact with GLY 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D TYR* 3.3 5.9 + - - -
90D LYS 3.1 14.8 - - - -
91D GLY* 3.7 1.6 - - - -
104D VAL* 1.3 80.5 - - - +
106D ASN* 1.3 64.6 + - - -
115D PRO* 3.3 9.0 - - - +
116D LEU 2.9 37.4 + - - -
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Residues in contact with ASN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ASN 3.7 1.0 - - - +
89D TYR* 3.5 8.6 - - - -
90D LYS* 2.9 33.0 + - + +
105D GLY* 1.3 79.1 - - - +
107D LEU* 1.3 60.4 - - - +
108D THR* 4.0 1.6 + - - -
113D THR* 3.8 22.7 - - + +
114D LYS* 3.4 4.5 - - - -
115D PRO* 3.4 26.9 - - - +
116D LEU 4.3 0.2 - - - +
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ALA* 4.6 1.6 - - + -
88D ASN 3.5 16.2 - - - +
89D TYR* 4.0 6.2 - - + -
106D ASN* 1.3 72.7 - - - +
108D THR* 1.3 67.8 - - - +
109D LEU* 4.1 23.6 - - + -
112D VAL 3.4 2.8 - - - +
113D THR* 3.2 2.4 - - - -
114D LYS 2.9 33.5 + - - +
116D LEU* 4.0 30.2 - - + +
144D PHE* 4.4 14.1 - - + -
149D PHE* 3.5 23.1 - - + -
201D OTP 3.8 38.4 - - + -
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Residues in contact with THR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D GLN 4.4 3.0 - - - +
87D ALA* 3.2 10.4 - - - +
88D ASN* 2.8 52.1 + - - +
106D ASN 4.0 1.4 + - - -
107D LEU* 1.3 72.5 - - - +
109D LEU* 1.4 61.3 + - - +
111D GLY* 4.6 13.5 - - - +
112D VAL 3.4 7.6 - - - +
113D THR* 2.7 30.9 + - - +
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Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ILE* 4.3 6.5 - - + -
79D PHE* 4.1 18.6 - - + -
86D GLN 5.2 0.9 - - - +
87D ALA* 4.2 8.5 - - + +
107D LEU* 4.0 13.9 - - + -
108D THR* 1.4 75.9 - - - +
110D HIS* 1.3 76.3 + - - +
111D GLY 3.0 0.9 - - - -
112D VAL 2.9 17.2 + - - +
144D PHE* 3.8 32.5 - - + -
149D PHE* 3.5 26.5 - - + +
151D LEU* 3.8 22.7 - - + -
201D OTP 3.7 32.3 - - + -
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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