Contacts of the strand formed by residues 84 - 99 (chain K) in PDB entry 5XS0
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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A SER* 3.7 12.1 + - - -
121A HIS* 3.6 36.1 + + - -
157A SER* 3.6 28.9 - - - -
26K PHE* 3.9 2.5 - - - -
72K ILE* 4.0 12.3 - - + -
75K ALA* 3.6 33.7 - - + -
76K ASN* 2.6 29.5 + - - +
79K PHE* 3.8 15.7 - - + -
80K GLY 3.1 24.2 - - - -
81K TYR 4.1 3.2 + - - +
83K GLY* 1.3 80.7 - - - +
85K ALA* 1.3 71.8 + - - +
86K HIS* 4.4 2.5 - - - -
113K VAL* 4.4 4.9 - - + -
114K GLN 3.5 6.5 - - - +
115K LEU* 4.1 8.1 - - + -
151K LEU* 4.0 22.2 - - + -
155K LEU* 3.9 28.0 - - + -
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Residues in contact with ALA 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 3.0 49.8 - - + +
121A HIS* 3.8 4.9 - - - -
26K PHE* 3.5 20.2 - - + -
84K TRP* 1.3 75.8 - - - +
86K HIS* 1.3 57.2 + - - +
113K VAL* 3.1 8.7 - - - +
114K GLN 2.6 35.5 + - - +
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Residues in contact with HIS 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 3.5 13.4 + - - -
121A HIS* 2.9 43.6 + + + -
122A GLU 2.9 45.9 + - - -
123A ASP* 4.3 8.2 + - + -
157A SER* 3.9 15.7 - - - -
84K TRP* 4.4 2.9 - + + -
85K ALA* 1.3 76.6 - - - +
87K SER* 1.3 61.4 + - - +
88K ILE* 5.4 1.6 - - + -
111K VAL* 3.8 15.7 - - + -
112K ARG 3.2 7.9 - - - +
113K VAL* 3.8 22.0 - - + -
147K VAL* 5.3 4.2 - - + +
151K LEU* 3.7 31.7 - - + +
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Residues in contact with SER 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ARG* 5.3 5.2 - - - -
120A TYR* 3.7 21.5 + - - -
122A GLU* 3.5 17.5 - - - -
86K HIS* 1.3 77.0 - - - +
88K ILE* 1.3 64.3 + - - +
89K THR* 3.5 2.9 + - - -
111K VAL* 3.4 6.4 - - - +
112K ARG* 2.9 47.3 + - - +
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Residues in contact with ILE 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A THR* 5.8 1.6 - - - +
110A PHE* 3.9 25.2 - - + -
122A GLU* 2.8 34.4 + - + +
123A ASP* 3.8 24.9 - - - +
124A VAL* 3.7 28.5 - - + -
86K HIS* 5.4 0.9 - - + -
87K SER* 1.3 73.6 - - - +
89K THR* 1.3 64.3 + - - +
90K GLN* 4.0 19.7 - - - +
91K GLN* 4.2 3.8 - - + +
109K ALA* 5.0 0.9 - - + -
110K PHE 3.6 9.2 - - - +
111K VAL* 4.9 5.6 - - + -
147K VAL* 3.8 22.2 - - + -
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Residues in contact with THR 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J ILE 5.6 2.0 - - - +
87K SER* 3.5 4.3 + - - -
88K ILE* 1.3 74.0 - - - +
90K GLN* 1.3 64.9 + - + +
110K PHE* 2.8 15.8 + - + -
112K ARG* 3.8 20.8 - - - +
122K GLU* 3.1 28.7 + - - +
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Residues in contact with GLN 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K ILE* 3.4 6.8 - - - +
89K THR* 1.3 87.7 - - + +
91K GLN* 1.3 68.3 + - - +
92K ASN* 4.0 18.5 - - - +
109K ALA* 3.5 0.3 - - - -
110K PHE* 2.8 52.8 + - + +
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Residues in contact with GLN 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PHE* 3.6 32.7 - - + -
124A VAL* 4.0 2.8 - - - +
88K ILE* 4.2 2.8 - - + +
90K GLN* 1.3 80.7 - - - +
92K ASN* 1.3 63.7 + - - +
107K VAL* 3.8 17.2 - - + +
108K CYS 3.4 9.2 - - - +
109K ALA* 3.7 12.2 - - + +
143K ARG* 2.5 65.0 + - - +
146K ALA* 4.1 0.2 - - - +
147K VAL* 3.3 27.9 - - - +
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Residues in contact with ASN 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J ARG* 4.9 4.9 - - - +
90K GLN* 4.0 18.2 - - - +
91K GLN* 1.3 74.8 - - - +
93K VAL* 1.3 74.0 + - - +
94K ASP* 3.2 26.7 + - - +
107K VAL* 4.3 1.6 - - - -
108K CYS* 3.0 46.5 + - - -
110K PHE* 5.6 0.9 - - + -
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Residues in contact with VAL 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ASP* 5.1 0.4 - - - +
92K ASN* 1.3 78.5 + - - +
94K ASP* 1.3 65.7 + - - +
95K PHE* 3.9 9.4 - - - +
96K VAL* 3.9 28.3 - - + -
107K VAL* 3.7 26.0 - - + -
139K LEU* 4.3 7.6 - - + -
143K ARG* 3.2 39.2 - - - +
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Residues in contact with ASP 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93J VAL* 5.1 0.5 - - - +
139J LEU* 3.8 19.4 - - + +
143J ARG* 2.8 32.5 + - - -
92K ASN* 3.2 25.0 + - - +
93K VAL* 1.3 75.0 - - - +
95K PHE* 1.3 64.8 + - + +
106K GLY 2.9 9.5 + - - +
108K CYS* 4.1 0.8 - - - +
126K TYR* 2.6 40.5 + - - +
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Residues in contact with PHE 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J LYS* 3.7 29.2 - - + +
136J ALA* 3.6 34.8 - - + -
139J LEU* 3.7 31.9 - - + -
93K VAL* 3.5 3.0 - - - +
94K ASP* 1.3 79.9 - - + +
96K VAL* 1.3 69.5 + - - +
97K ASP* 3.5 18.8 - - - +
104K TYR* 3.2 31.0 - - + -
105K VAL* 3.6 5.8 - - - +
106K GLY* 3.3 38.8 + - - +
126K TYR* 3.9 0.7 - - - -
130K GLU* 6.0 0.7 - - - -
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Residues in contact with VAL 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93K VAL* 3.9 17.9 - - + -
95K PHE* 1.3 80.3 - - - +
97K ASP* 1.3 66.5 + - - +
98K LEU 4.4 0.3 + - - -
103K PHE* 4.4 9.6 - - + -
104K TYR 4.0 3.1 - - - -
105K VAL* 4.2 13.5 - - + -
135K LYS* 3.9 29.8 - - + +
139K LEU* 4.1 19.3 - - + -
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Residues in contact with ASP 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J LYS* 2.8 38.5 + - - -
95K PHE* 3.5 10.8 - - - +
96K VAL* 1.3 81.0 + - - +
98K LEU* 1.3 60.9 + - - +
99K ASN* 4.0 16.6 - - - +
102K LYS 3.8 0.3 - - - +
103K PHE* 3.5 11.1 - - - -
104K TYR* 3.1 38.0 + - + +
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Residues in contact with LEU 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K ASP* 1.3 73.8 - - - +
99K ASN* 1.3 66.5 + - - +
100K ASN 4.2 1.1 + - - +
101K GLY* 3.7 30.7 - - - +
102K LYS 3.6 12.8 - - - +
103K PHE* 3.8 31.6 - - + -
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Residues in contact with ASN 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K ASP* 4.0 13.5 + - - +
98K LEU* 1.3 76.9 - - - +
100K ASN* 1.3 84.1 + - - +
101K GLY 3.2 0.7 - - - -
102K LYS* 3.0 25.1 + - - +
104K TYR* 3.6 32.9 + - + +
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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