Contacts of the strand formed by residues 102 - 115 (chain D) in PDB entry 5XRZ
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 ALA 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D LEU* 3.3 4.2 - - - +
99D ASN 3.0 34.7 + - - +
100D ASN* 3.3 4.0 - - - +
101D GLY* 1.3 77.5 - - - +
103D PHE* 1.3 59.9 + - - +
104D TYR* 3.3 30.0 - - + +
130D GLU 4.1 7.2 - - - +
131D GLY* 4.3 7.6 - - - +
132D LEU 4.0 4.3 - - - -
133D ALA* 4.9 0.2 - - - +
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Residues in contact with PHE 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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96D VAL* 4.9 6.3 - - + -
97D ASP 3.5 13.9 - - - -
98D LEU* 3.6 39.3 - - + -
101D GLY 5.5 0.4 - - - -
102D ALA* 1.3 72.0 - - - +
104D TYR* 1.3 60.7 + - - +
105D VAL* 4.8 3.1 - - + -
129D SER 3.0 11.8 - - - +
130D GLU 3.0 15.8 - - - +
132D LEU 3.1 14.4 + - - +
133D ALA* 3.4 21.1 - - - -
134D SER 3.7 0.7 - - - -
135D LYS* 3.3 63.7 - - + -
138D SER* 3.8 16.5 + - - +
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Residues in contact with TYR 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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95D PHE* 3.5 18.4 - - + -
96D VAL* 3.7 0.5 - - - -
97D ASP* 3.0 40.0 + - + +
99D ASN* 3.3 40.2 + - + +
100D ASN* 5.6 1.4 + - - -
102D ALA* 3.3 40.7 - - + +
103D PHE* 1.3 71.4 - - - +
105D VAL* 1.3 61.1 + - - +
129D SER 3.6 3.4 - - - -
130D GLU* 3.3 46.7 - - + +
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Residues in contact with VAL 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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136C ALA* 4.6 0.5 - - - +
95D PHE* 3.6 12.8 - - - +
96D VAL* 3.9 20.9 - - + -
103D PHE* 4.7 4.9 - - + -
104D TYR* 1.3 80.2 - - - +
106D GLY* 1.3 60.6 + - - +
107D VAL* 3.8 17.0 - - + -
127D GLY 3.9 0.5 - - - +
128D VAL* 3.8 9.4 - - - +
129D SER 3.1 29.6 + - - +
130D GLU* 5.4 1.1 - - - +
135D LYS* 5.3 2.0 - - + +
138D SER* 3.8 27.8 - - - +
139D LEU* 3.6 30.1 - - + -
142D ALA* 4.0 8.4 - - + +
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Residues in contact with GLY 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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136C ALA* 4.6 1.1 - - - -
93D VAL* 3.6 0.3 - - - +
94D ASP 2.8 22.4 + - - -
95D PHE* 3.2 32.2 + - - +
105D VAL* 1.3 72.6 - - - +
107D VAL* 1.3 66.1 + - - +
126D TYR* 3.7 24.7 - - - -
127D GLY 3.9 0.9 - - - -
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Residues in contact with VAL 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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91D GLN* 3.9 17.0 - - + +
92D ASN 4.0 6.5 - - - +
93D VAL* 3.7 26.5 - - + -
94D ASP 4.3 0.4 - - - +
105D VAL* 3.8 7.0 - - + -
106D GLY* 1.3 80.2 - - - +
108D CYS* 1.3 70.4 + - - +
126D TYR* 3.3 11.4 - - - -
127D GLY 2.8 32.8 + - - -
139D LEU* 4.7 1.1 - - + -
142D ALA* 3.7 27.6 - - + +
143D ARG* 3.9 27.8 - - + -
146D ALA* 3.6 4.0 - - + +
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Residues in contact with CYS 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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143C ARG* 2.8 44.2 - - - +
91D GLN* 3.4 8.5 - - - +
92D ASN* 3.1 45.6 + - - -
94D ASP* 4.3 0.2 + - - -
107D VAL* 1.3 74.9 - - - +
109D ALA* 1.3 62.2 + - - +
110D PHE* 3.7 18.2 - - - -
124D VAL* 4.3 4.7 - - + -
125D GLY 3.3 7.6 - - - +
126D TYR* 3.6 16.8 - - + -
146D ALA* 4.0 2.7 - - - -
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Residues in contact with ALA 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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88D ILE* 4.8 2.7 - - + -
90D GLN 3.6 6.3 - - - -
91D GLN* 3.7 12.1 - - + +
108D CYS* 1.3 74.9 - - - +
110D PHE* 1.3 65.9 + - - +
111D VAL* 4.1 3.1 - - + -
124D VAL* 3.2 7.8 - - - +
125D GLY 2.8 31.7 + - - -
146D ALA* 3.9 15.5 - - + +
147D VAL* 3.7 32.1 - - + -
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Residues in contact with PHE 110 (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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88C ILE* 3.7 29.8 - - + -
91C GLN* 3.4 45.1 - - + -
143C ARG* 4.5 4.7 - - - -
88D ILE* 3.6 4.0 - - - +
89D THR* 2.8 35.8 + - + -
90D GLN* 2.9 41.8 + - + +
92D ASN* 5.8 1.6 - - + -
108D CYS* 3.7 23.3 - - - -
109D ALA* 1.3 76.6 - - - +
111D VAL* 1.3 60.0 + - - +
122D GLU* 4.0 13.2 - - - +
123D ASP 3.7 3.6 - - - +
124D VAL* 3.5 22.4 - - + -
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Residues in contact with VAL 111 (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 HIS* 3.6 34.5 - - + -
87D SER 3.3 10.8 - - - +
88D ILE* 5.2 3.1 - - + -
109D ALA* 4.8 1.3 - - + -
110D PHE* 1.3 79.0 - - - +
112D ARG* 1.3 63.5 + - - +
113D VAL* 4.1 1.6 - - + -
122D GLU* 3.2 3.5 - - - +
123D ASP 3.0 30.4 + - - +
147D VAL* 3.4 38.8 - - + +
150D GLY* 3.5 17.0 - - - +
151D LEU* 3.5 18.6 - - + +
154D ALA* 3.7 4.5 - - + +
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Residues in contact with ARG 112 (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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87C SER* 4.9 4.9 - - - -
85D ALA 3.8 0.5 - - - +
86D HIS* 3.2 2.3 - - - -
87D SER* 2.9 42.9 + - - +
89D THR* 4.0 18.8 - - - +
110D PHE 4.1 0.2 + - - -
111D VAL* 1.3 73.1 - - - +
113D VAL* 1.3 68.6 + - - +
114D GLN* 3.2 30.7 + - - +
120D TYR* 3.3 47.0 - - + +
121D HIS 3.4 8.5 - - - +
122D GLU* 3.9 17.9 - - + -
120E TYR* 4.5 12.1 + - - -
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Residues in contact with VAL 113 (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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84D TRP* 3.8 15.3 - - + -
85D ALA 3.1 13.0 - - - +
86D HIS* 4.0 2.7 - - + -
111D VAL* 4.6 0.9 - - + -
112D ARG* 1.3 74.6 - - - +
114D GLN* 1.3 63.8 + - - +
120D TYR* 3.1 4.2 - - - +
121D HIS* 2.7 41.0 + - - +
151D LEU* 3.7 25.4 - - + -
154D ALA* 3.6 25.6 - - + +
155D LEU* 3.8 28.5 - - + +
158D PHE* 4.1 17.2 - - + -
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Residues in contact with GLN 114 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D PHE* 3.1 25.8 - - + -
27D GLY* 5.2 5.0 - - - -
84D TRP* 3.6 0.2 - - - -
85D ALA 2.6 34.3 + - - +
112D ARG* 3.2 27.2 + - - +
113D VAL* 1.3 76.5 - - - +
115D LEU* 1.3 71.3 + - - +
118D GLY* 3.7 18.1 + - - +
119D SER 3.2 17.3 - - - +
120D TYR* 4.2 6.1 - - + -
120E TYR* 3.2 29.6 + - - +
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C TYR* 3.9 19.5 - - + -
82C ASN* 4.6 1.1 - - + -
26D PHE* 3.6 4.5 - - - -
27D GLY 4.5 0.2 + - - -
31D TYR* 3.9 8.1 - - + +
79D PHE* 3.9 35.2 - - + -
83D GLY 3.3 14.1 - - - +
84D TRP* 4.0 6.1 - - + -
113D VAL* 5.1 0.4 - - + -
114D GLN* 1.3 86.5 - - - +
116D LYS* 1.3 59.0 + - - +
117D ASP* 3.0 20.6 - - - +
118D GLY* 2.9 19.4 + - - -
119D SER* 2.8 14.4 + - - +
158D PHE* 3.6 44.4 - - + -
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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
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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