Contacts of the strand formed by residues 97 - 109 (chain E) in PDB entry 2YGD
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 VAL 97 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92E LYS* 4.3 1.7 - - - +
93E VAL* 3.7 5.5 - - - +
94E LEU* 2.9 64.6 + - + +
95E GLY 4.4 1.1 - - - +
96E ASP* 1.3 87.0 - - - +
98E ILE* 1.3 59.6 + - - +
99E GLU* 4.3 22.0 - - + +
122E TYR 3.4 20.9 - - - +
123E ARG* 4.0 17.9 - - + -
128E VAL* 4.9 1.3 - - - -
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Residues in contact with ILE 98 (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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79E LEU* 4.1 13.7 - - + -
91E VAL* 4.0 13.5 - - + -
92E LYS 3.5 17.5 - - - +
93E VAL* 4.0 15.5 - - + -
96E ASP 4.3 0.4 + - - -
97E VAL* 1.3 71.5 - - - +
99E GLU* 1.3 67.8 + - - +
122E TYR* 3.1 55.0 + - + +
124E ILE* 4.3 1.8 - - + -
128E VAL* 4.0 24.4 - - + +
135E SER* 3.9 10.1 - - - +
143E LEU* 5.0 0.9 - - + -
145E VAL* 3.5 36.1 - - + -
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Residues in contact with GLU 99 (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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79E LEU* 4.8 1.1 - - - -
91E VAL* 3.8 2.3 - - - +
92E LYS* 2.6 76.9 + - + +
97E VAL* 4.3 17.6 - - + +
98E ILE* 1.3 84.1 - - - +
100E VAL* 1.3 66.7 + - - +
101E HIS 4.2 0.2 - - - -
119E HIS* 2.7 36.5 + - + +
120E ARG 3.5 8.5 - - - +
121E LYS* 3.6 13.4 - - + +
122E TYR 4.4 2.7 - - - +
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Residues in contact with VAL 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E LEU* 3.8 19.0 - - + +
80E ASP 4.5 0.7 - - - +
81E VAL* 4.1 19.5 - - + -
89E LEU* 4.2 13.7 - - + -
90E LYS 3.9 3.1 - - - -
91E VAL* 4.0 10.1 - - + -
99E GLU* 1.3 78.4 - - - +
101E HIS* 1.3 57.9 + - - +
118E PHE 3.7 0.6 - - - +
119E HIS* 3.5 10.8 - - - -
120E ARG* 2.8 51.2 + - + +
143E LEU* 3.5 37.5 - - + -
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Residues in contact with HIS 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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88E GLU 5.4 0.2 + - - -
89E LEU* 3.6 5.1 - - - +
90E LYS* 2.8 66.1 + - + +
92E LYS* 5.6 6.4 - - + +
99E GLU* 4.2 0.4 - - - +
100E VAL* 1.3 72.1 - - - +
102E GLY* 1.3 66.3 + - - +
103E LYS* 3.7 26.9 + - + -
117E GLU* 2.7 31.1 + - + -
118E PHE 3.6 4.9 - - - -
119E HIS* 4.8 16.4 - + + -
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Residues in contact with GLY 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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81E VAL* 5.4 1.0 - - - +
84E PHE* 3.5 21.8 - - - -
88E GLU 3.2 9.0 - - - -
89E LEU* 4.3 5.6 - - - +
101E HIS* 1.3 77.0 + - - +
103E LYS* 1.3 60.3 + - - +
117E GLU* 3.1 9.5 - - - +
118E PHE* 2.7 36.3 + - - +
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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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84E PHE* 3.7 1.6 - - - -
88E GLU* 2.8 30.0 + - - +
101E HIS* 3.7 16.4 - - + -
102E GLY* 1.3 73.6 - - - +
104E HIS* 1.3 65.3 + - - +
115E SER* 5.0 9.2 - - - +
116E ARG 3.5 5.2 - - - +
117E GLU* 3.6 29.8 - - + +
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Residues in contact with HIS 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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84E PHE* 3.2 30.4 - + + -
88E GLU* 3.5 28.7 + - + +
103E LYS* 1.3 75.0 - - - +
105E GLU* 1.3 90.7 + - + +
106E GLU* 3.3 28.0 + - - +
115E SER* 3.3 7.7 - - - -
116E ARG* 2.9 36.0 + - - +
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Residues in contact with GLU 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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104E HIS* 1.3 93.8 + - + +
106E GLU* 1.3 64.8 + - - +
107E ARG 3.3 3.6 - - - +
108E GLN* 3.5 42.5 + - + +
113E PHE* 3.3 18.3 - - - +
114E ILE 2.9 33.9 + - - +
115E SER* 3.9 6.5 + - - +
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Residues in contact with GLU 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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83B HIS* 5.5 1.2 + - - -
118B PHE* 3.6 19.4 - - + -
104E HIS* 3.3 21.7 + - - -
105E GLU* 1.3 73.6 - - - +
107E ARG* 1.3 75.8 + - + +
114E ILE* 2.8 30.6 + - + +
115E SER 4.2 0.4 - - - -
116E ARG* 2.7 66.9 + - + +
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Residues in contact with ARG 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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80B ASP* 4.3 11.9 + - - -
81B VAL* 5.7 0.6 - - - +
82B LYS* 4.8 17.3 - - - +
83B HIS* 5.9 1.8 + - - -
118B PHE* 5.3 8.5 - - - -
120B ARG* 3.5 25.1 - - - +
105E GLU* 3.3 4.7 - - - +
106E GLU* 1.3 94.4 + - - +
108E GLN* 1.3 66.2 + - - +
114E ILE* 3.0 65.9 + - + +
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Residues in contact with GLN 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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105E GLU* 3.5 41.5 + - + +
107E ARG* 1.3 74.2 - - - +
109E ASP* 1.3 64.1 + - - +
112E GLY 3.7 5.2 - - - -
113E PHE* 3.7 23.1 - - + -
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Residues in contact with ASP 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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120B ARG* 4.7 0.9 + - - -
122B TYR* 3.0 37.6 + - - -
108E GLN* 1.3 75.4 - - - +
110E GLU* 1.3 73.2 + - + +
111E HIS* 3.6 0.5 - - - -
112E GLY* 2.8 34.2 + - - +
113E PHE* 4.4 6.1 - - - -
114E ILE* 3.7 24.8 - - - +
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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
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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