Contacts of the strand formed by residues 97 - 103 (chain E) in PDB entry 5ITX
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 ALA 97 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30E SER* 4.2 2.9 - - - -
93E LEU* 4.5 2.5 - - + -
94E PRO* 3.0 22.6 + - + +
95E ARG 3.2 0.6 + - - -
96E HIS* 1.3 73.8 - - - +
98E HIS* 1.3 59.7 + - - +
99E LEU 3.5 2.5 - - - -
100E ARG* 2.5 46.0 + - + +
113E CYS* 3.8 32.3 - - + -
114E PHE 3.5 7.9 - - - -
115E VAL* 4.3 3.8 - - - +
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Residues in contact with HIS 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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28E GLU 4.7 0.2 - - - -
29E LYS* 3.7 1.0 - - - +
30E SER* 3.2 33.7 + - - +
32E VAL* 4.3 11.7 - - + -
33E SER* 4.4 9.2 - - - -
96E HIS* 2.6 48.8 + - + +
97E ALA* 1.3 73.3 + - - +
99E LEU* 1.3 59.4 + - - +
100E ARG* 5.2 0.2 - - - -
114E PHE* 3.1 13.4 + + + +
116E ASP* 3.5 15.1 + - + -
119E ARG* 2.8 51.2 + - + +
123E TRP* 3.2 29.3 - + + -
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Residues in contact with LEU 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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27E VAL* 3.7 21.3 - - + +
28E GLU 3.4 17.3 - - - +
29E LYS* 4.0 2.9 - - - +
38E VAL* 3.9 16.2 - - + -
75E LEU* 4.8 2.0 - - + -
77E PHE* 3.8 25.1 - - + -
97E ALA 3.5 0.4 + - - -
98E HIS* 1.3 80.9 - - - +
100E ARG* 1.3 67.5 + - - +
101E PHE* 4.1 17.6 - - + -
113E CYS* 3.3 3.6 - - - -
114E PHE* 2.7 40.8 + - + +
123E TRP* 3.4 43.5 - - + +
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Residues in contact with ARG 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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26E CYS 4.3 0.5 - - - +
27E VAL* 3.4 10.9 - - - +
28E GLU* 2.7 56.6 + - + +
29E LYS 3.3 24.0 + - - -
30E SER* 3.6 15.2 - - - +
93E LEU* 3.7 32.8 - - + +
97E ALA* 2.5 37.9 + - + +
99E LEU* 1.3 80.2 - - - +
101E PHE* 1.3 65.3 + - - +
102E TYR* 3.8 22.8 + - + -
111E ALA* 5.6 0.7 - - + -
112E LEU 3.4 4.7 - - - +
113E CYS* 4.0 16.6 - - - -
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Residues in contact with PHE 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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23E PHE* 3.4 23.5 - - + -
26E CYS 4.8 2.7 - - - -
27E VAL* 3.3 35.4 - - + -
45E TYR* 4.1 7.4 - - - +
47E ILE* 4.3 2.7 - - + -
58E LEU* 4.4 19.3 - - + -
60E LEU* 3.8 35.0 - - + -
75E LEU* 4.5 7.6 - - + -
77E PHE* 4.8 1.3 - + - -
85E PHE* 4.9 3.8 - + - -
99E LEU* 4.1 30.3 - - + -
100E ARG* 1.3 74.1 - - - +
102E TYR* 1.3 61.5 + - - +
111E ALA* 3.6 1.6 - - - -
112E LEU* 2.8 66.8 + - + +
114E PHE 4.8 5.8 - - - -
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Residues in contact with TYR 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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23E PHE* 3.4 7.2 - - - +
24E GLY 2.9 33.5 + - - +
25E GLY* 6.0 0.2 - - - -
26E CYS* 4.2 18.6 + - + +
28E GLU* 3.1 37.4 + - + -
45E TYR* 4.2 2.9 + - - -
90E ARG* 3.8 51.2 + - + +
93E LEU* 3.6 21.9 - - + +
100E ARG* 3.8 14.3 + - + -
101E PHE* 1.3 74.1 - - - +
103E THR* 1.3 65.8 + - - +
110E LEU 4.1 1.8 - - - -
111E ALA* 3.6 28.5 - - + -
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Residues in contact with THR 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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21E LEU* 4.5 19.1 - - + -
22E VAL 3.8 13.9 - - - +
23E PHE* 3.9 26.9 - - + +
24E GLY 3.8 5.0 - - - +
87E LEU* 5.5 0.4 - - + -
90E ARG* 5.8 1.2 + - - -
102E TYR* 1.3 80.2 - - - +
104E ALA* 1.3 63.1 + - - +
105E PRO* 4.7 0.5 - - - +
107E GLY* 5.9 0.4 - - - -
108E PRO* 2.8 27.4 + - - +
109E ARG* 4.2 1.0 - - - -
110E LEU* 3.2 35.4 + - + +
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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