Contacts of the strand formed by residues 84 - 99 (chain I) 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 TRP 84 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26I PHE* 3.9 1.6 - - - -
72I ILE* 4.3 7.9 - - + -
75I ALA* 3.8 24.7 - - + -
76I ASN* 3.1 31.9 + - - +
79I PHE* 3.8 18.2 - - + -
80I GLY 3.0 24.5 - - - -
81I TYR 4.2 3.1 + - - +
83I GLY* 1.3 77.9 - - - +
85I ALA* 1.3 72.8 + - - +
86I HIS* 4.2 4.9 - - + -
113I VAL* 3.9 16.6 - - + -
114I GLN 3.5 6.3 - - - +
115I LEU* 4.1 7.6 - - + -
151I LEU* 3.8 39.0 - - + -
155I LEU* 4.1 12.1 - - + -
119J SER* 3.4 15.6 + - - -
121J HIS* 3.5 28.0 + + - -
157J SER* 3.4 27.8 - - - -
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Residues in contact with ALA 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I PHE* 3.5 19.7 - - + -
84I TRP* 1.3 82.1 - - - +
86I HIS* 1.3 58.6 + - - +
112I ARG 3.8 0.3 - - - +
113I VAL* 3.1 4.2 - - - +
114I GLN* 2.6 37.9 + - - +
120J TYR* 3.1 48.0 - - + +
121J HIS* 3.7 4.5 - - - -
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Residues in contact with HIS 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I TRP* 4.2 3.9 - + + -
85I ALA* 1.3 74.6 - - - +
87I SER* 1.3 63.1 + - - +
88I ILE* 5.5 0.4 - - + -
111I VAL* 3.7 21.1 - - + -
112I ARG 3.2 9.6 - - - +
113I VAL* 4.2 4.0 - - + -
147I VAL* 5.0 4.9 - - + +
151I LEU* 3.6 37.2 - - + +
120J TYR* 3.3 20.9 + - - +
121J HIS* 2.9 34.3 + - + -
122J GLU 2.8 47.6 + - - -
123J ASP* 4.2 11.4 + - + -
154J ALA 5.4 0.4 - - - -
157J SER* 3.9 14.3 + - - -
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Residues in contact with SER 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I HIS* 1.3 78.1 - - - +
88I ILE* 1.3 66.3 + - - +
89I THR* 3.5 2.3 + - - -
111I VAL* 3.3 7.6 - - - +
112I ARG* 2.9 49.2 + - - +
112J ARG* 5.0 4.5 - - - -
120J TYR* 3.5 24.6 + - - -
122J GLU* 3.6 15.5 - - - -
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Residues in contact with ILE 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I HIS* 5.5 0.4 - - + -
87I SER* 1.3 72.1 - - - +
89I THR* 1.3 68.1 + - - +
90I GLN* 4.1 20.1 - - - +
91I GLN* 4.2 5.2 - - + +
109I ALA* 4.9 0.4 - - + -
110I PHE 3.5 10.1 - - - +
111I VAL* 4.7 3.6 - - + +
147I VAL* 3.7 20.4 - - + -
89J THR* 5.9 1.2 - - - +
110J PHE* 3.7 35.7 - - + -
122J GLU* 2.7 37.2 + - + +
123J ASP* 3.7 21.1 - - - +
124J VAL* 3.7 18.2 - - + -
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Residues in contact with THR 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H ILE 5.8 1.8 - - - +
87I SER* 3.5 3.0 + - - -
88I ILE* 1.3 74.0 - - - +
90I GLN* 1.3 65.7 + - + +
110I PHE* 2.7 17.5 + - + -
112I ARG* 3.8 22.0 - - - +
122I GLU* 3.0 28.3 + - - +
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Residues in contact with GLN 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I ILE* 3.4 5.3 - - - -
89I THR* 1.3 87.5 - - + +
91I GLN* 1.3 70.9 + - - +
92I ASN* 4.9 9.1 - - + +
110I PHE* 2.9 48.0 + - + +
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Residues in contact with GLN 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I ILE* 4.2 5.7 - - + +
90I GLN* 1.3 80.1 - - - +
92I ASN* 1.3 63.1 + - - +
107I VAL* 4.2 8.6 - - + +
108I CYS 3.5 11.9 + - - +
109I ALA* 3.9 6.5 - - + +
143I ARG* 2.4 67.9 + - - +
147I VAL* 3.3 30.9 - - - +
110J PHE* 3.3 26.9 - - + -
124J VAL* 3.7 5.4 - - - +
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Residues in contact with ASN 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H ARG* 4.9 5.1 - - - +
90I GLN* 5.0 12.1 - - + +
91I GLN* 1.3 75.2 - - - +
93I VAL* 1.3 78.7 + - - +
94I ASP* 3.4 15.2 + - - +
107I VAL* 4.7 1.6 - - - -
108I CYS* 3.2 41.3 + - - +
110I PHE* 5.8 2.0 - - + -
143I ARG* 5.4 0.4 - - - +
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Residues in contact with VAL 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I ASN* 1.3 82.5 + - - +
94I ASP* 1.3 66.3 + - - +
95I PHE 3.8 15.7 - - - +
96I VAL* 4.0 16.2 - - + -
106I GLY 3.7 5.2 - - - +
107I VAL* 3.7 28.5 - - + -
139I LEU* 4.4 9.6 - - + -
143I ARG* 3.8 32.7 - - - +
94J ASP* 4.8 4.5 - - - +
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Residues in contact with ASP 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H VAL* 4.8 5.5 - - - +
139H LEU* 3.8 19.4 - - + +
143H ARG* 2.8 34.4 + - - -
92I ASN* 3.4 12.4 + - - +
93I VAL* 1.3 74.8 - - - +
95I PHE* 1.3 62.9 + - + +
106I GLY 2.9 12.0 + - - +
108I CYS* 3.9 4.2 + - - +
126I TYR* 2.6 37.9 + - - +
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Residues in contact with PHE 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H LYS* 3.5 34.8 - - + +
136H ALA* 3.3 32.8 - - + -
139H LEU* 3.6 32.5 - - + -
93I VAL* 3.5 3.6 - - - +
94I ASP* 1.3 80.3 - - + +
96I VAL* 1.3 69.6 + - - +
97I ASP* 3.1 25.8 - - - +
104I TYR* 3.6 21.1 - - + -
105I VAL* 3.6 2.0 - - - -
106I GLY* 3.1 50.2 + - - +
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Residues in contact with VAL 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I VAL* 4.0 9.6 - - + -
95I PHE* 1.3 80.7 - - - +
97I ASP* 1.3 70.6 + - - +
103I PHE* 4.6 5.6 - - + -
104I TYR 3.5 4.5 - - - -
105I VAL* 3.9 22.0 - - + -
135I LYS* 4.1 28.0 - - + +
139I LEU* 3.9 20.6 - - + -
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Residues in contact with ASP 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H LYS* 3.5 23.2 + - - -
95I PHE* 3.1 27.5 - - - +
96I VAL* 1.3 82.8 + - - +
98I LEU* 1.3 62.7 + - - +
99I ASN* 4.3 8.1 - - - +
103I PHE* 3.4 11.1 - - - -
104I TYR* 2.8 43.3 + - + +
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Residues in contact with LEU 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ASP* 1.3 76.6 - - - +
99I ASN* 1.3 68.2 + - - +
100I ASN 4.0 1.6 + - - +
101I GLY* 3.7 15.9 - - - +
102I ALA 3.3 31.2 - - - +
103I PHE* 3.6 36.6 - - + -
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Residues in contact with ASN 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ASP* 5.0 7.0 - - - +
98I LEU* 1.3 81.9 + - - +
100I ASN* 1.3 86.7 + - - +
101I GLY 3.3 1.1 - - - -
102I ALA* 2.9 25.5 + - - +
104I TYR* 3.2 35.6 + - + +
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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