Contacts of the strand formed by residues 102 - 115 (chain J) 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 LYS 102 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98J LEU* 3.4 6.0 - - - -
99J ASN 2.8 35.7 + - - +
100J ASN* 4.4 11.4 - - - +
101J GLY* 1.3 83.1 - - - +
103J PHE* 1.3 59.9 + - - +
104J TYR* 3.6 18.2 - - + +
131J GLY* 3.2 40.0 + - - +
132J LEU 3.5 3.6 - - - +
133J LYS* 4.7 11.7 - - + +
7Z C 4.8 1.7 + - - +
8Z C 2.5 46.0 + - - +
9Z C 4.2 15.0 + - - -
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Residues in contact with PHE 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J VAL* 4.0 15.5 - - + -
97J ASP 3.3 11.9 - - - -
98J LEU* 3.9 33.9 - - + -
101J GLY 4.8 1.3 - - - -
102J LYS* 1.3 72.7 - - - +
104J TYR* 1.3 63.3 + - - +
105J VAL* 4.5 3.1 - - + -
129J SER 3.1 12.9 - - - +
131J GLY 3.1 17.5 + - - -
132J LEU 2.9 11.8 + - - +
133J LYS* 3.4 23.3 - - - -
134J SER 3.9 0.2 - - - -
135J LYS* 3.5 57.2 - - + -
138J SER* 3.7 20.9 + - - +
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Residues in contact with TYR 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J PHE* 3.1 20.7 - - + -
97J ASP* 3.0 40.3 + - + +
99J ASN* 3.8 28.8 + - + +
100J ASN* 5.4 1.2 + - - -
102J LYS* 3.6 34.3 - - + +
103J PHE* 1.3 78.3 - - - +
105J VAL* 1.3 60.0 + - - +
129J SER 3.4 3.8 - - - -
130J GLU* 3.0 38.6 - - + +
131J GLY 4.6 2.9 - - - -
6Z C 3.9 18.4 - - + -
7Z C 3.4 26.0 + - - -
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Residues in contact with VAL 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I ALA* 4.3 0.3 - - - +
95J PHE* 3.4 14.7 - - - +
96J VAL* 3.9 24.7 - - + -
103J PHE* 4.5 2.2 - - + -
104J TYR* 1.3 80.4 - - - +
106J GLY* 1.3 62.0 + - - +
107J VAL* 4.0 12.1 - - + -
127J GLY 3.7 0.2 - - - +
128J VAL* 3.4 10.9 - - - +
129J SER 3.0 31.0 + - - +
130J GLU* 4.9 1.0 - - - +
135J LYS* 5.5 0.4 - - + +
138J SER* 3.8 27.4 - - - +
139J LEU* 4.0 17.9 - - + +
142J ALA* 3.7 24.0 - - + -
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Residues in contact with GLY 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I ALA* 4.5 0.9 - - - -
93J VAL 3.7 0.2 - - - -
94J ASP* 2.7 31.7 + - - +
95J PHE* 3.3 32.4 + - - +
105J VAL* 1.3 74.3 - - - +
107J VAL* 1.3 60.8 + - - +
126J TYR* 3.7 17.3 - - - -
127J GLY 3.5 4.3 - - - -
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Residues in contact with VAL 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J GLN* 3.7 36.3 - - + +
92J ASN 3.6 8.1 - - - +
93J VAL* 3.7 22.2 - - + -
105J VAL* 4.0 9.0 - - + -
106J GLY* 1.3 78.9 - - - +
108J CYS* 1.3 65.9 + - - +
126J TYR* 3.4 7.4 - - - -
127J GLY 2.8 35.9 + - - -
139J LEU* 4.8 1.1 - - + -
142J ALA* 3.7 27.8 - - + +
143J ARG* 4.0 15.3 - - + -
146J ALA* 3.2 4.2 - - + +
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Residues in contact with CYS 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I ARG* 3.5 39.0 - - - +
91J GLN* 3.3 7.1 - - - +
92J ASN* 2.8 56.6 + - - +
94J ASP* 4.0 1.5 + - - -
107J VAL* 1.3 73.4 - - - +
109J ALA* 1.3 58.5 + - - +
110J PHE* 3.9 14.8 - - + -
124J VAL* 4.9 2.5 - - + -
125J GLY 3.4 7.9 - - - +
126J TYR* 3.5 21.6 - - + -
146J ALA* 4.1 1.3 - - - -
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Residues in contact with ALA 109 (chain J).
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* 4.9 2.2 - - + -
90J GLN 3.3 7.9 - - - +
91J GLN* 3.5 25.1 - - + +
108J CYS* 1.3 74.2 - - - +
110J PHE* 1.3 65.4 + - - +
111J VAL* 4.0 5.3 + - + -
123J ASP 3.9 0.3 - - - +
124J VAL* 3.4 5.4 - - - +
125J GLY 2.9 31.3 + - - +
146J ALA 3.8 21.5 - - - +
147J VAL* 3.9 10.8 - - + +
150J GLY* 4.8 0.3 - - - -
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Residues in contact with PHE 110 (chain J).
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* 4.1 23.1 - - + -
91I GLN* 3.6 46.2 - - + -
143I ARG* 4.4 5.2 - - - -
88J ILE* 3.5 3.6 - - - -
89J THR* 2.7 36.5 + - + -
90J GLN* 2.6 44.1 + - + +
92J ASN* 5.7 0.2 - - + -
108J CYS* 3.9 23.6 - - - -
109J ALA* 1.3 76.2 - - - +
111J VAL* 1.3 59.0 + - - +
122J GLU* 3.9 14.8 - - - +
123J ASP 3.6 4.5 - - - +
124J VAL* 3.5 22.4 - - + -
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Residues in contact with VAL 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J HIS* 3.7 34.8 - - + -
87J SER 3.3 8.3 - - - +
88J ILE* 4.7 6.7 - - + -
109J ALA* 4.7 3.6 - - + -
110J PHE* 1.3 78.7 - - - +
112J ARG* 1.3 62.6 + - - +
113J VAL* 4.6 1.8 - - + -
122J GLU* 3.3 3.2 - - - +
123J ASP 3.1 29.9 + - - +
147J VAL* 3.6 37.5 - - + +
150J GLY* 3.8 15.5 - - - +
151J LEU* 3.8 18.6 - - + +
154J ALA* 3.9 4.9 - - - +
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Residues in contact with ARG 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I SER* 4.9 5.6 - - - -
86J HIS* 3.2 3.0 - - - -
87J SER* 2.9 41.6 + - - +
89J THR* 4.1 14.1 - - - +
110J PHE 4.2 0.6 + - - -
111J VAL* 1.3 73.0 - - - +
113J VAL* 1.3 69.4 + - - +
114J GLN* 3.5 30.1 + - + +
120J TYR* 4.0 41.8 - - + +
121J HIS 3.5 4.9 - - - +
122J GLU* 3.9 24.7 - - + +
120K TYR* 4.7 11.6 + - - +
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Residues in contact with VAL 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J TRP* 4.3 11.7 - - + -
85J ALA 3.1 10.3 - - - +
86J HIS* 3.8 5.2 - - + -
111J VAL* 4.1 1.1 - - + -
112J ARG* 1.3 75.1 - - - +
114J GLN* 1.3 66.2 + - - +
115J LEU* 5.0 0.4 - - + -
120J TYR* 3.1 6.9 - - - +
121J HIS 2.8 35.9 + - - +
151J LEU* 3.6 31.9 - - + -
154J ALA* 3.6 19.7 - - + -
155J LEU* 3.8 16.4 - - + -
158J PHE* 3.8 28.7 - - + -
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Residues in contact with GLN 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J PHE* 3.5 20.4 - - + -
27J GLY* 4.8 6.8 - - - -
84J TRP* 3.4 2.4 - - - +
85J ALA 2.7 39.8 + - - +
112J ARG* 3.5 24.1 + - - +
113J VAL* 1.3 73.9 - - - +
115J LEU* 1.3 76.5 + - - +
118J GLY* 3.6 21.9 + - - +
119J SER 3.2 12.6 - - - +
120J TYR* 4.4 5.2 - - + -
120K TYR* 3.2 30.0 + - - +
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Residues in contact with LEU 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I TYR* 3.9 19.1 - - + -
82I ASN* 4.6 0.7 - - + -
26J PHE* 3.6 6.3 - - - -
27J GLY* 4.4 0.3 - - - -
31J TYR* 4.2 7.9 - - + +
79J PHE* 3.6 45.8 - - + -
83J GLY 3.3 9.4 - - - +
84J TRP* 3.8 11.7 - - + -
113J VAL* 5.0 0.4 - - + -
114J GLN* 1.3 84.6 - - - +
116J LYS* 1.3 60.8 + - - +
117J ASP* 2.9 15.9 + - - +
118J GLY 3.0 11.0 + - - -
119J SER* 2.8 33.5 + - - +
158J PHE* 3.6 30.3 - - + -
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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