Contacts of the strand formed by residues 102 - 115 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98I LEU* 3.5 3.1 - - - -
99I ASN 2.9 29.1 + - - +
100I ASN* 4.4 9.6 - - - +
101I GLY* 1.3 83.2 - - - +
103I PHE* 1.3 62.8 + - - +
104I TYR* 3.2 26.8 - - + +
131I GLY* 3.1 37.4 + - - +
132I LEU 3.7 2.9 - - - -
133I LYS* 4.3 16.8 - - + +
2Z C 3.0 57.7 + - - +
3Z C 4.3 7.3 + - - -
4Z C 4.2 10.5 - - - +
5Z C 5.1 1.6 - - - +
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Residues in contact with PHE 103 (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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96I VAL* 4.3 8.1 - - + -
97I ASP 3.3 13.0 - - - -
98I LEU* 3.7 36.6 - - + -
101I GLY 5.1 0.9 - - - -
102I LYS* 1.3 71.9 - - - +
104I TYR* 1.3 62.6 + - - +
105I VAL* 4.2 4.5 - - + -
129I SER 3.5 6.5 - - - +
131I GLY 3.4 19.4 + - - -
132I LEU 2.9 14.3 + - - +
133I LYS* 3.3 29.4 - - - -
135I LYS* 3.4 57.4 - - + -
138I SER* 3.9 18.2 + - - +
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Residues in contact with TYR 104 (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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95I PHE* 3.1 22.8 - - + -
97I ASP* 3.1 31.3 + - + +
99I ASN* 3.8 30.9 + - + +
100I ASN* 4.9 4.3 + - - -
102I LYS* 3.2 46.0 - - + +
103I PHE* 1.3 77.3 - - - +
105I VAL* 1.3 61.2 + - - +
129I SER 3.5 4.7 - - - -
130I GLU* 3.7 33.2 - - + +
131I GLY* 4.2 9.4 - - - -
2Z C 4.8 3.3 + - - -
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Residues in contact with VAL 105 (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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136H ALA* 4.2 1.3 - - - +
95I PHE* 3.5 14.1 - - - +
96I VAL* 4.1 23.6 - - + -
103I PHE* 4.8 2.0 - - + -
104I TYR* 1.3 80.9 - - - +
106I GLY* 1.3 61.3 + - - +
107I VAL* 3.8 13.2 - - + -
127I GLY 3.8 0.5 - - - +
128I VAL* 3.6 9.7 - - - +
129I SER* 3.1 29.9 + - - +
130I GLU* 5.4 0.4 - - - +
135I LYS* 5.3 0.9 - - + +
138I SER* 3.9 27.8 - - - +
139I LEU* 3.9 18.8 - - + +
142I ALA* 3.7 24.0 - - + -
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Residues in contact with GLY 106 (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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136H ALA* 4.2 1.3 - - - -
93I VAL 3.8 0.2 - - - -
94I ASP* 2.8 31.7 + - - +
95I PHE* 3.4 23.7 + - - +
105I VAL* 1.3 74.8 - - - +
107I VAL* 1.3 60.1 + - - +
126I TYR* 3.6 24.5 - - - -
127I GLY 3.7 4.3 - - - -
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Residues in contact with VAL 107 (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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91I GLN* 3.8 28.5 - - + +
92I ASN 3.6 9.0 - - - +
93I VAL* 3.7 23.6 - - + +
105I VAL* 3.8 9.9 - - + -
106I GLY* 1.3 78.6 - - - +
108I CYS* 1.3 71.7 + - - +
126I TYR* 3.4 7.5 - - - -
127I GLY 2.8 35.8 + - - -
139I LEU* 5.0 0.7 - - + -
142I ALA* 3.8 26.5 - - + +
143I ARG* 4.1 11.0 - - + -
146I ALA* 3.3 8.6 - - + +
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Residues in contact with CYS 108 (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* 3.4 42.0 - - - +
91I GLN* 3.4 1.9 - - - -
92I ASN* 2.8 55.0 + - - +
94I ASP* 4.0 0.8 + - - -
107I VAL* 1.3 79.2 - - - +
109I ALA* 1.3 61.5 + - - +
110I PHE* 3.9 12.8 - - - -
124I VAL* 4.1 5.2 - - + -
125I GLY 3.3 8.5 - - - +
126I TYR* 3.7 20.7 - - + -
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Residues in contact with ALA 109 (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* 4.8 2.0 - - + -
90I GLN 3.3 8.7 - - - +
91I GLN* 3.9 18.2 - - + +
108I CYS* 1.3 74.5 - - - +
110I PHE* 1.3 65.0 + - - +
111I VAL* 3.9 6.2 + - + -
124I VAL* 3.2 6.2 - - - +
125I GLY 2.9 31.5 + - - -
146I ALA 3.8 27.4 - - - +
147I VAL* 4.0 9.9 - - + +
150I GLY* 4.8 0.2 - - - -
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Residues in contact with PHE 110 (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* 3.9 21.1 - - + -
91H GLN* 3.7 43.1 - - + -
143H ARG* 4.3 5.8 - - - -
88I ILE* 3.6 3.3 - - - -
89I THR* 2.7 35.3 + - + -
90I GLN* 2.7 50.3 + - + +
108I CYS* 3.9 21.1 - - - -
109I ALA* 1.3 74.7 - - - +
111I VAL* 1.3 58.9 + - - +
122I GLU* 3.7 15.7 - - - +
123I ASP 3.5 5.2 - - - +
124I VAL* 3.5 30.1 - - + -
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Residues in contact with VAL 111 (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* 3.8 30.3 - - + -
87I SER 3.5 7.0 - - - +
88I ILE* 4.7 11.4 - - + -
109I ALA* 3.9 6.9 - - + -
110I PHE* 1.3 76.7 - - - +
112I ARG* 1.3 63.2 + - - +
113I VAL* 4.1 2.0 - - + -
122I GLU* 3.3 2.3 - - - -
123I ASP 3.0 29.9 + - - +
147I VAL* 3.6 32.5 - - + +
150I GLY* 3.6 15.5 - - - -
151I LEU* 3.7 23.6 - - + +
154I ALA* 3.8 5.4 - - - +
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Residues in contact with ARG 112 (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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87H SER* 4.7 6.3 + - - -
85I ALA 4.0 0.2 - - - +
86I HIS* 3.2 2.9 - - - -
87I SER* 3.0 40.5 + - - +
89I THR* 4.0 13.0 - - - +
110I PHE 4.1 0.4 + - - -
111I VAL* 1.3 72.3 - - - +
113I VAL* 1.3 70.2 + - - +
114I GLN* 3.2 34.0 + - + +
120I TYR* 3.7 46.4 - - + +
121I HIS 3.4 3.8 - - - +
122I GLU* 3.7 27.8 - - + +
120J TYR* 4.6 6.0 + - - -
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Residues in contact with VAL 113 (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* 4.1 11.7 - - + -
85I ALA 3.2 10.5 - - - +
86I HIS* 3.9 3.8 - - + -
111I VAL* 4.7 0.7 - - + -
112I ARG* 1.3 74.3 - - - +
114I GLN* 1.3 67.4 + - - +
120I TYR* 3.1 5.2 - - - +
121I HIS 2.7 42.3 + - - +
151I LEU* 3.6 27.8 - - + -
154I ALA* 3.6 22.9 - - + -
155I LEU* 3.7 28.0 - - + +
158I PHE* 3.8 19.5 - - + -
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Residues in contact with GLN 114 (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* 3.4 23.8 - - + -
27I GLY* 4.7 5.8 - - - -
84I TRP* 3.4 2.3 - - - +
85I ALA 2.6 40.2 + - - +
112I ARG* 3.2 26.8 + - - +
113I VAL* 1.3 75.8 - - - +
115I LEU* 1.3 71.7 + - - +
118I GLY* 3.6 20.4 + - - +
119I SER 3.2 15.9 - - - +
120I TYR* 4.3 4.7 - - + -
158I PHE* 5.5 0.2 - - - -
120J TYR* 3.6 25.8 + - - +
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Residues in contact with LEU 115 (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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81H TYR* 3.9 19.1 - - + -
82H ASN* 4.7 0.9 - - + -
26I PHE* 3.6 7.4 - - - -
27I GLY* 4.3 0.2 - - - -
31I TYR* 4.5 5.2 - - + +
79I PHE* 3.7 44.9 - - + -
83I GLY 3.4 4.3 - - - +
84I TRP* 3.9 18.4 - - + -
113I VAL* 4.9 0.4 - - + -
114I GLN* 1.3 83.7 - - - +
116I LYS* 1.3 58.8 + - - +
117I ASP* 2.9 28.9 + - - +
118I GLY 3.0 12.2 + - - -
119I SER* 2.7 14.9 + - - +
158I PHE* 3.6 37.7 - - + -
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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