Contacts of the strand formed by residues 99 - 110 (chain E) in PDB entry 3J7Y
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 LEU 99 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98E GLY* 1.3 79.5 - - - +
100E ILE* 1.3 68.9 + - - +
101E ALA 3.9 0.9 - - - +
124E VAL* 3.4 40.2 - - + -
127E CYS* 4.5 1.8 - - + -
147E VAL* 4.9 2.5 - - - -
179E PHE* 3.5 4.1 - - - -
193E LEU* 3.3 34.8 - - + -
194E TYR 3.4 22.2 - - - +
195E ALA* 4.2 0.7 - - - -
197E HIS* 4.2 8.5 - - + +
198E PHE* 3.3 33.9 - - + -
283E ILE* 5.0 0.2 - - + -
298E LYS* 3.5 3.5 - - - -
299E VAL* 2.8 36.6 + - + +
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Residues in contact with ILE 100 (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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99E LEU* 1.3 80.6 - - - +
101E ALA* 1.3 58.5 + - - +
102E LEU* 5.0 2.4 - - - +
125E GLN 4.1 4.9 + - - +
127E CYS* 3.0 27.6 - - - +
147E VAL* 3.8 12.3 - - + +
148E GLY 3.1 29.4 - - - +
149E GLY* 3.9 10.0 - - - -
175E THR* 3.6 18.6 - - - +
177E LYS* 3.5 51.1 - - + +
179E PHE* 4.8 2.9 - - + -
296E LEU* 4.0 14.4 - - + -
297E VAL 3.3 13.0 - - - +
298E LYS* 4.9 3.4 - - + -
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Residues in contact with ALA 101 (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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99E LEU* 3.9 1.7 - - + -
100E ILE* 1.3 74.3 - - - +
102E LEU* 1.3 62.5 + - - +
103E LYS 4.0 0.2 - - - -
122E LEU* 3.8 22.9 - - + -
123E GLN 3.3 22.0 - - - +
124E VAL* 4.0 11.9 - - + +
296E LEU* 3.4 4.7 - - - -
297E VAL* 2.7 40.7 + - + +
299E VAL* 4.2 13.4 - - + +
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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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100E ILE 5.0 2.0 - - - +
101E ALA* 1.3 75.2 - - - +
103E LYS* 1.3 65.8 + - - +
104E LEU* 3.1 9.8 + - + -
122E LEU* 3.3 2.7 - - - -
123E GLN* 2.8 41.6 + - + +
125E GLN* 3.4 45.8 - - + +
150E LYS* 3.5 33.7 - - + +
294E ASN* 3.3 30.5 - - - +
295E CYS 3.4 0.9 - - - -
296E LEU* 3.4 21.8 - - + -
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Residues in contact with LYS 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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3148A C 3.1 24.4 + - - -
3149A C 4.3 7.2 - - - -
101E ALA 3.9 2.0 + - - -
102E LEU* 1.3 69.4 - - - +
104E LEU* 1.3 56.5 + - - +
105E GLY* 4.6 5.6 - - - +
106E MET* 4.9 9.6 - - - -
120E THR* 4.1 22.9 - - - +
122E LEU* 3.7 18.2 - - + +
289E VAL* 2.8 32.2 + - + +
290E PRO 4.1 8.5 - - - +
291E GLY 2.9 16.8 + - - +
292E HIS 3.4 22.7 - - - +
293E LYS* 4.5 6.5 - - - +
294E ASN* 2.6 35.0 + - - -
295E CYS 3.0 11.0 + - - +
297E VAL* 4.3 8.4 - - + +
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Residues in contact with LEU 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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102E LEU* 3.1 11.5 + - + +
103E LYS* 1.3 75.1 - - - +
105E GLY* 1.3 58.1 + - - +
121E LEU* 2.8 24.1 + - + +
123E GLN* 3.9 32.3 - - + +
125E GLN* 5.3 1.1 - - - +
282E ILE* 3.5 30.5 - - + -
293E LYS* 3.7 15.4 - - - +
294E ASN* 4.0 7.1 - - - +
87Q THR* 3.7 17.5 + - - -
88Q ASP* 3.9 34.2 + - + +
90Q LEU* 4.3 10.3 - - + -
91Q LYS* 4.3 22.4 - - + +
94Q ILE* 5.0 1.3 - - + -
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Residues in contact with GLY 105 (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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3150A U 5.2 0.7 - - - -
103E LYS* 3.8 4.8 - - - +
104E LEU* 1.3 81.8 - - - +
106E MET* 1.3 66.3 + - - -
120E THR* 3.4 4.8 + - - -
121E LEU* 2.8 26.3 + - - +
293E LYS* 4.5 15.0 - - - -
87Q THR* 5.3 0.7 - - - -
91Q LYS* 3.8 17.1 - - - +
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Residues in contact with MET 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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3148A C 3.3 28.3 - - - +
3149A C 4.0 15.3 - - - +
3150A U 3.1 60.7 + - + +
3164A C 5.9 0.7 - - - +
103E LYS* 4.9 8.7 - - - -
105E GLY* 1.3 78.3 - - - +
107E MET* 1.3 63.3 + - - +
118E VAL* 3.5 12.1 - - + -
119E VAL 3.2 8.7 - - - +
120E THR* 3.6 16.4 - - - -
287E GLY 3.4 18.2 - - - +
288E SER* 3.8 12.8 - - - +
91Q LYS* 3.1 20.8 + - - +
95Q GLU* 4.8 0.3 - - - -
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Residues in contact with MET 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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3150A U 3.4 11.2 - - - -
106E MET* 1.3 77.6 - - - +
108E PRO* 1.4 77.4 - - + +
109E LEU* 6.0 3.4 - - + -
118E VAL* 4.6 0.2 - - - -
119E VAL* 2.8 34.7 + - + +
121E LEU* 3.5 40.2 - - + -
275E ARG* 4.2 4.5 - - - +
284E TYR* 4.0 18.4 - - + +
91Q LYS* 4.3 1.3 - - - -
94Q ILE* 4.5 5.8 - - + -
95Q GLU* 3.9 30.5 - - + +
98Q ASP* 4.0 13.0 - - + +
145Q LEU* 3.5 28.5 - - + -
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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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3150A U 3.4 21.5 - - - +
3151A A 6.6 0.2 - - - -
107E MET* 1.4 92.2 - - + +
109E LEU* 1.3 60.5 + - - +
110E TRP* 3.8 28.7 - - + -
116E LYS* 3.7 26.5 - - + +
117E HIS 3.8 4.7 - - - +
118E VAL* 4.3 3.6 - - - -
95Q GLU* 5.2 0.4 - - - +
145Q LEU* 3.4 30.6 - - + +
146Q GLY* 3.8 18.8 - - - +
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Residues in contact with LEU 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 MET* 6.0 2.9 - - + -
108E PRO* 1.3 74.9 - - - +
110E TRP* 1.3 73.3 + - - +
111E THR* 4.7 3.1 - - + -
115E GLN 3.5 0.7 - - - +
116E LYS* 3.7 2.8 - - - -
117E HIS* 2.8 34.2 + - + +
119E VAL* 3.4 23.1 - - + -
274E TRP* 3.6 49.1 - - + +
275E ARG* 4.9 22.0 - - + +
284E TYR* 5.2 4.5 - - + -
337E VAL* 3.7 33.4 - - + -
145Q LEU* 5.5 0.9 - - - -
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Residues in contact with TRP 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* 3.8 33.0 - - + -
109E LEU* 1.3 78.1 - - - +
111E THR* 1.3 56.7 + - - +
115E GLN 3.2 26.0 - - - +
116E LYS* 3.3 18.3 - - + +
337E VAL* 3.7 5.7 - - - +
338E CYS* 2.8 37.5 + - + +
145Q LEU* 3.5 38.8 - - + -
165Q GLU* 3.4 23.3 - - + -
167Q TYR* 3.1 27.4 - - + -
168Q ASN* 2.8 29.2 + - - -
169Q PRO* 3.3 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