Contacts of the strand formed by residues 103 - 115 (chain E) in PDB entry 1H2I
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 PHE 103 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96E VAL* 4.3 13.0 - - + -
97E ASP 3.2 14.6 - - - -
98E LEU* 3.7 33.9 - - + -
101E GLY 4.9 0.9 - - - -
102E LYS* 1.3 72.0 - - - +
104E TYR* 1.3 64.8 + - - +
105E VAL* 4.1 4.7 - - + -
129E SER 3.4 7.0 - - - +
131E GLY 3.0 22.9 + - - -
132E LEU 2.9 11.4 + - - +
133E LYS* 3.2 31.0 - - - -
134E SER 3.8 1.8 - - - -
135E LYS* 3.4 52.9 - - + -
138E SER* 3.7 20.1 + - - +
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Residues in contact with TYR 104 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95E PHE* 3.2 17.2 - - + -
96E VAL* 3.5 0.2 - - - -
97E ASP* 2.6 48.5 + - + +
99E ASN* 4.0 25.1 - - + +
100E ASN* 3.4 25.2 + - - -
102E LYS* 3.4 33.7 - - + +
103E PHE* 1.3 72.0 - - - +
105E VAL* 1.3 60.2 + - - +
129E SER 3.4 2.5 - - - -
130E GLU* 3.6 34.1 - - + +
131E GLY* 3.7 17.1 - - - -
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Residues in contact with VAL 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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136D ALA* 4.9 0.4 - - - -
95E PHE* 3.5 13.9 - - - +
96E VAL* 4.2 20.4 - - + -
103E PHE* 4.5 2.0 - - + -
104E TYR* 1.3 84.8 - - - +
106E GLY* 1.3 62.2 + - - +
107E VAL* 4.0 6.7 - - + -
127E GLY 3.7 0.5 - - - +
128E VAL* 3.4 10.2 - - - +
129E SER* 2.8 42.7 + - - +
130E GLU* 4.9 1.2 - - - +
135E LYS* 5.6 0.4 - - - +
138E SER* 3.9 24.5 - - - +
139E LEU* 3.6 28.7 - - + -
142E ALA* 3.9 15.2 - - + +
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Residues in contact with GLY 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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136D ALA* 4.6 0.9 - - - -
94E ASP* 2.7 32.9 + - - +
95E PHE* 3.3 23.8 + - - +
105E VAL* 1.3 74.7 - - - +
107E VAL* 1.3 60.0 + - - +
126E TYR* 3.4 25.1 - - - -
127E GLY 3.6 4.0 - - - -
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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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91E GLN* 3.6 35.9 - - + +
92E ASN 3.5 12.3 - - - +
93E VAL* 3.7 23.3 - - + -
94E ASP 4.3 0.2 - - - +
105E VAL* 4.0 9.2 - - + -
106E GLY* 1.3 79.1 - - - +
108E CYS* 1.3 64.1 + - - +
126E TYR* 3.2 9.3 - - - -
127E GLY 2.6 38.4 + - - -
139E LEU* 4.7 0.7 - - + -
142E ALA* 3.8 26.0 - - + +
143E ARG* 4.0 11.0 - - + -
146E ALA* 3.4 4.3 - - + +
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Residues in contact with CYS 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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143D ARG* 3.2 42.8 - - - -
91E GLN* 3.2 6.2 - - - +
92E ASN* 2.9 49.0 + - - -
94E ASP* 4.7 0.4 + - - -
107E VAL* 1.3 74.4 - - - +
109E ALA* 1.3 61.5 + - - +
110E PHE* 3.8 16.2 - - - -
124E VAL* 4.4 5.6 - - + -
125E GLY 3.2 7.6 - - - +
126E TYR* 3.6 20.1 - - + -
146E ALA* 4.1 2.0 - - - -
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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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88E ILE* 4.9 2.2 - - + -
90E GLN 3.3 8.7 - - - +
91E GLN* 4.0 11.2 - - + +
108E CYS* 1.3 77.5 - - - +
110E PHE* 1.3 65.4 + - - +
111E VAL* 3.9 7.3 + - + +
123E ASP 3.7 0.3 - - - +
124E VAL* 3.2 5.4 - - - +
125E GLY 2.7 31.7 + - - -
146E ALA* 3.8 29.4 - - + +
147E VAL* 4.0 13.0 - - + +
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Residues in contact with PHE 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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88D ILE* 3.8 30.7 - - + -
91D GLN* 3.2 44.4 - - + -
143D ARG* 4.5 3.6 - - - -
88E ILE* 3.5 5.5 - - - -
89E THR* 2.8 47.5 + - - +
90E GLN* 2.8 40.1 + - + +
92E ASN* 5.6 0.4 - - + -
108E CYS* 3.8 23.6 - - - -
109E ALA* 1.3 72.4 - - - +
111E VAL* 1.3 57.9 + - - +
122E GLU* 3.8 6.1 - - - +
123E ASP 3.4 2.5 - - - +
124E VAL* 3.1 24.7 - - + -
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Residues in contact with VAL 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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86E HIS* 3.9 25.1 - - + -
87E SER 3.4 12.1 - - - +
88E ILE* 4.6 9.4 - - + -
109E ALA* 4.5 7.9 - - + -
110E PHE* 1.3 76.3 - - - +
112E ARG* 1.3 63.1 + - - +
113E VAL 4.8 0.9 - - - +
122E GLU* 3.2 4.6 - - - -
123E ASP 3.0 30.9 + - - -
147E VAL* 3.6 30.3 - - + +
150E GLY* 3.8 17.3 - - - +
151E LEU* 3.7 23.6 - - + +
154E ALA* 3.7 7.0 - - + +
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Residues in contact with ARG 112 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D SER* 5.1 5.4 - - - -
86E HIS* 3.2 3.3 - - - -
87E SER* 2.9 38.0 + - - +
89E THR* 4.0 23.8 - - + +
110E PHE 4.2 0.4 + - - -
111E VAL* 1.3 72.0 - - - +
113E VAL* 1.3 64.6 + - - +
114E GLN* 2.9 34.2 + - - +
118E GLY 4.8 0.4 + - - -
120E TYR* 3.5 47.0 - - + +
121E HIS 3.6 6.3 - - - +
122E GLU* 3.9 24.7 - - + -
120F TYR* 5.0 5.4 + - - -
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Residues in contact with VAL 113 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84E TRP* 4.1 11.4 - - + -
85E ALA 3.1 14.4 - - - +
86E HIS* 4.0 7.6 - - + -
111E VAL* 5.3 0.2 - - + -
112E ARG* 1.3 74.3 - - - +
114E GLN* 1.3 67.5 + - - +
120E TYR* 3.2 7.1 - - - +
121E HIS 3.0 42.1 + - - +
151E LEU* 4.7 3.4 - - + -
154E ALA* 3.3 32.5 - - + +
155E LEU* 3.6 25.1 - - + +
158E PHE* 4.1 18.0 - - + -
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Residues in contact with GLN 114 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E PHE* 3.4 15.4 - - + -
27E GLY* 3.5 29.7 - - - -
84E TRP* 3.1 3.6 - - - +
85E ALA 2.7 38.4 + - - +
112E ARG* 2.9 26.0 + - - +
113E VAL* 1.3 75.4 - - - +
115E LEU* 1.3 74.8 + - - +
118E GLY* 3.6 13.7 - - - +
119E SER 3.2 15.0 - - - +
120E TYR* 4.3 2.9 - - + -
158E PHE* 5.4 0.2 - - - -
120F TYR* 3.2 22.7 + - - +
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Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D TYR* 4.1 23.6 - - + -
26E PHE* 3.5 5.9 - - - -
31E TYR* 3.7 14.8 - - + +
79E PHE* 4.1 14.8 - - + -
83E GLY 3.3 9.9 - - - +
84E TRP* 3.9 12.6 - - + -
113E VAL* 5.0 0.4 - - + -
114E GLN* 1.3 89.3 + - - +
116E LYS* 1.3 60.8 + - - +
117E ASP* 2.8 14.6 + - + -
118E GLY 2.9 10.4 + - - -
119E SER* 3.0 30.5 + - - +
158E PHE* 3.2 47.3 - - + -
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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