Contacts of the strand formed by residues 99 - 116 (chain E) in PDB entry 4S0H
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 99 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PRO* 6.1 3.9 - - + +
111A ASP* 5.8 5.9 - - - +
97E LYS 4.5 6.5 - - - +
98E THR* 1.3 83.1 - - - +
100E TYR* 1.3 62.2 + - - +
142E PRO* 5.1 11.0 - - + -
143E ALA* 3.6 9.2 - - - +
144E THR* 4.9 13.2 - - + -
187E LYS 3.7 0.7 - - - -
188E ALA* 3.3 42.0 + - + +
189E ASP 4.0 15.7 + - - +
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Residues in contact with TYR 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E ILE* 5.0 0.2 - - - +
94E LEU* 3.6 31.3 - - + +
95E ASN* 3.7 31.3 + - - +
98E THR* 3.8 26.0 - - + +
99E LYS* 1.3 78.4 - - - +
101E ILE* 1.3 63.4 + - - +
102E LEU* 4.3 5.6 - - + -
142E PRO* 3.2 4.6 - - - +
143E ALA 2.8 30.6 + - - +
145E GLY* 3.9 11.7 - - - -
148E TRP* 3.4 21.3 + - + +
185E ILE* 3.5 18.8 - - + -
186E VAL 3.2 20.4 - - - +
187E LYS* 4.3 3.1 - - + -
188E ALA* 5.2 0.2 - - - -
199E THR 4.3 11.4 + - - -
200E ALA* 3.8 23.0 - - + +
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Residues in contact with ILE 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 4.9 9.6 - - - +
107A VAL* 6.1 2.9 - - + -
133A GLY* 4.0 26.2 - - - -
134A ARG 4.7 2.0 - - - +
135A LEU* 4.8 10.8 - - + -
100E TYR* 1.3 75.5 - - - +
102E LEU* 1.3 65.0 + - - +
103E LEU* 4.1 18.8 - - + -
137E VAL* 4.1 14.1 - - + -
141E SER* 3.8 14.6 - - - +
142E PRO* 4.0 18.6 - - + -
184E HIS 3.7 0.7 - - - +
185E ILE* 3.5 3.8 - - - -
186E VAL* 2.9 45.7 + - + +
187E LYS 4.5 9.8 + - - +
188E ALA* 5.1 3.1 - - + -
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E VAL* 5.4 0.2 - - + -
91E VAL* 4.5 14.1 - - + -
94E LEU* 5.6 2.0 - - + -
100E TYR* 4.2 2.4 - - + -
101E ILE* 1.3 78.8 - - - +
103E LEU* 1.3 62.1 + - - +
137E VAL* 3.8 0.9 - - - +
138E HIS* 2.8 27.6 + - + +
141E SER* 3.0 13.8 + - - +
148E TRP* 3.6 42.3 - - + +
153E VAL* 4.0 31.9 - - + -
155E PHE* 4.3 6.5 - - + -
183E LEU* 4.1 16.2 - - + -
184E HIS 3.6 2.5 - - - +
185E ILE* 3.9 31.0 - - + -
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 6.3 1.1 - - + -
135A LEU* 4.2 23.3 - - + -
101E ILE* 4.1 13.5 - - + -
102E LEU* 1.3 75.3 - - - +
104E MET* 1.3 63.5 + - - +
135E LEU* 4.1 23.1 - - + -
136E TYR 3.1 13.5 - - - +
137E VAL* 3.8 15.3 - - + -
155E PHE* 4.1 5.4 - - - -
183E LEU* 3.3 10.0 - - - +
184E HIS* 3.0 57.8 + - + +
186E VAL* 3.8 27.6 - - + -
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Residues in contact with MET 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E MET* 4.6 9.2 - - + -
87E TYR* 3.3 40.2 - - + -
103E LEU* 1.3 79.4 - - - +
105E ASP* 1.3 63.7 + - - +
106E ILE* 3.7 21.3 - - + -
135E LEU* 3.4 7.1 - - - +
136E TYR 2.7 30.3 + - - +
155E PHE* 3.8 22.7 - - + -
158E LEU* 3.5 33.9 - - + -
171E ILE* 4.9 0.7 - - - -
181E PRO* 4.5 7.6 - - + -
182E ARG 3.0 24.2 - - - +
183E LEU* 4.2 4.7 - - + -
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Residues in contact with ASP 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 4.2 7.1 - - - +
104E MET* 1.3 76.9 - - - +
106E ILE* 1.3 68.2 + - - +
107E VAL* 3.4 7.8 - - - +
133E GLY 5.9 0.4 - - - +
134E ARG 3.8 7.0 - - - +
135E LEU* 3.5 20.9 - - + +
171E ILE* 4.1 7.6 - - - -
181E PRO* 3.6 1.6 - - - +
182E ARG* 2.7 63.6 + - - +
184E HIS* 2.6 29.6 + - - -
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Residues in contact with ILE 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E MET* 5.1 3.1 - - - -
104E MET* 3.7 26.9 - - + -
105E ASP* 1.3 82.4 - - - +
107E VAL* 1.3 67.2 + - - +
108E PRO* 4.6 1.2 - - - +
133E GLY* 5.5 6.6 - - - -
134E ARG 4.8 1.5 + - - +
158E LEU* 4.6 7.6 - - + -
160E LEU* 4.8 6.1 - - + -
171E ILE* 4.0 24.7 - - + +
173E LEU* 3.6 21.6 - - + +
179E TYR* 3.6 38.3 - - + -
180E GLN 3.8 2.7 - - - +
181E PRO* 3.8 21.8 - - + -
211E PHE* 4.3 9.6 - - + -
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Residues in contact with VAL 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ILE* 4.9 4.0 - - + -
188A ALA* 4.4 23.6 - - + +
105E ASP* 3.4 16.6 - - + +
106E ILE* 1.3 77.0 - - - +
108E PRO* 1.3 73.0 - - + +
179E TYR* 3.6 4.6 - - - -
180E GLN* 2.7 55.6 + - + +
182E ARG* 3.3 44.2 - - + +
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Residues in contact with PRO 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ALA* 5.0 8.9 - - + +
106E ILE 4.6 1.8 - - - +
107E VAL* 1.3 95.7 - - + +
109E ALA* 1.3 63.8 + - - +
110E ASP* 4.3 12.9 - - - +
130E ALA* 4.7 20.0 - - + -
178E LYS 3.8 6.7 - - - +
179E TYR* 4.1 16.6 - - + -
180E GLN* 5.1 0.5 - - - +
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Residues in contact with ALA 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E VAL 3.5 3.1 + - - -
108E PRO* 1.3 72.6 - - - +
110E ASP* 1.3 63.8 + - - +
178E LYS* 2.8 55.7 + - + +
179E TYR 4.0 9.6 - - - +
180E GLN* 4.6 9.6 - - + +
210E ALA* 5.3 1.6 - - + -
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Residues in contact with ASP 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E PRO* 3.4 13.6 - - - +
109E ALA* 1.3 82.3 + - - +
111E ASP* 1.3 58.6 + - - +
112E HIS* 3.3 30.4 + - + +
114E TYR* 2.9 26.8 + - - -
127E ALA* 4.4 5.0 - - - +
177E HIS* 5.6 1.9 - - - +
178E LYS* 3.9 27.0 + - - +
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Residues in contact with ASP 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E ASP* 1.3 74.1 - - - +
112E HIS* 1.3 74.8 + - + +
125E GLY 4.1 2.6 - - - +
126E LYS* 3.9 15.7 + - - +
127E ALA* 3.0 30.8 + - - +
128E GLU 5.7 0.7 - - - -
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Residues in contact with HIS 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E ASP* 3.3 39.4 + - + +
111E ASP* 1.3 89.5 + - + +
113E ARG* 1.3 65.9 + - - +
114E TYR* 3.7 27.1 + - + +
123E VAL* 3.8 31.1 - - + +
125E GLY 3.5 7.6 - - - +
127E ALA* 3.5 8.5 - - - +
177E HIS* 3.9 16.6 - - - +
178E LYS 4.6 0.3 + - - -
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Residues in contact with ARG 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E HIS* 1.3 76.6 - - - +
114E TYR* 1.3 74.5 + - - +
123E VAL* 3.6 4.5 - - - -
124E THR* 3.0 32.6 + - + +
125E GLY* 3.3 17.8 + - - +
126E LYS 4.0 16.2 - - - +
127E ALA 4.0 1.4 - - - +
128E GLU* 4.7 13.3 + - - -
175E SER 4.8 2.6 + - - -
176E MET* 3.9 19.0 - - + +
177E HIS* 4.1 25.9 - - + -
2G C 5.5 5.5 + - - -
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Residues in contact with TYR 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E ASP* 2.9 26.4 + - - -
112E HIS* 3.7 26.4 + - + +
113E ARG* 1.3 80.8 + - - +
115E LYS* 1.4 61.2 + - - +
121E TRP* 3.5 29.2 - + + -
122E SER 3.2 28.0 - - - -
123E VAL* 3.8 19.5 - - + +
124E THR* 3.7 5.8 + - - -
176E MET* 3.0 43.8 + - - +
177E HIS 4.8 0.4 - - - -
178E LYS* 3.8 33.8 - - + +
212E ILE* 5.0 9.2 - - + -
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Residues in contact with LYS 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E TYR* 1.4 73.0 - - - +
116E PHE* 1.3 60.1 + - - +
117E ALA* 3.7 24.6 + - - +
118E ASP* 4.9 4.4 + - - -
120E LYS 4.0 0.5 - - - +
121E TRP* 3.8 6.3 - - - -
122E SER* 3.0 47.7 + - - -
123E VAL 5.5 0.2 - - - +
124E THR* 3.2 23.6 - - + +
176E MET* 4.9 1.8 - - - -
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Residues in contact with PHE 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E LYS* 1.3 74.4 - - - +
117E ALA* 1.3 70.4 + - - +
118E ASP 4.6 4.3 - - - -
119E ASN* 3.0 34.3 - - - -
120E LYS 3.3 15.0 - - - -
121E TRP* 3.5 36.8 - + + -
176E MET* 5.9 0.8 - - - -
218E GLN* 3.3 46.7 + - + +
219E ASN* 3.6 36.8 - - + -
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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
------------------------------------------------------------
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