Contacts of the strand formed by residues 18 - 23 (chain E) in PDB entry 3T30
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 18 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ILE* 3.4 49.6 - - + +
66D PRO* 6.6 0.2 - - + -
78D VAL* 4.3 23.1 - - + +
80D ILE* 6.2 0.2 - - + -
98D LEU* 4.4 9.6 - - + -
102D VAL* 5.9 0.2 - - + -
17E VAL* 1.3 91.4 - - + +
19E TRP* 1.3 61.8 + - - +
47E HIS* 5.5 2.0 - - - +
116E SER* 6.2 0.2 - - - -
117E GLY 3.3 17.3 - - - +
118E GLN* 3.4 24.2 - - + +
119E GLU* 5.1 0.2 - - - +
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Residues in contact with TRP 19 (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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78D VAL* 3.7 10.1 - - - +
18E LEU* 1.3 76.6 - - - +
20E GLY* 1.3 98.5 + - - +
21E CYS* 3.8 9.4 - - - -
30E TRP* 3.9 22.0 - + + -
32E PHE* 5.2 1.8 - + + -
44E LEU* 3.3 43.8 - - + +
45E LEU 3.4 2.7 + - - -
46E LEU* 4.0 14.4 - - + -
104E PHE* 4.0 16.4 - + - -
115E LEU* 3.9 21.1 - - + -
116E SER* 3.5 3.6 - - - -
117E GLY* 2.9 70.6 + - - +
118E GLN 3.1 6.0 - - - +
119E GLU* 3.4 33.0 - - + +
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Residues in contact with GLY 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D PRO 5.7 1.3 - - - -
78D VAL* 3.7 19.2 - - - +
19E TRP* 1.3 85.4 - - - +
21E CYS* 1.3 63.4 + - - +
30E TRP* 3.9 9.5 + - - -
115E LEU 3.1 12.6 - - - -
116E SER* 4.3 0.4 - - - -
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Residues in contact with CYS 21 (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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19E TRP* 3.8 4.0 - - - -
20E GLY* 1.3 69.6 - - - -
22E GLU* 1.3 59.3 + - - +
23E LEU* 4.3 4.7 - - - -
30E TRP* 2.9 68.2 - - + +
104E PHE* 4.6 5.4 - - - -
114E PHE* 3.2 8.3 - - - +
115E LEU* 2.8 60.1 + - - +
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Residues in contact with GLU 22 (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 CYS* 1.3 76.1 - - - +
23E LEU* 1.3 71.1 + - - +
24E SER* 5.4 4.4 - - - -
27E ARG* 4.3 9.0 - - - +
29E THR 5.2 0.3 - - - +
30E TRP* 4.7 5.7 - - - +
112E PRO* 3.5 28.7 - - + +
113E VAL 3.4 3.6 - - - +
114E PHE* 3.4 32.8 - - + -
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Residues in contact with LEU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E CYS* 4.3 2.5 - - - -
22E GLU* 1.3 78.7 - - - +
24E SER* 1.3 61.6 + - - +
27E ARG 3.5 2.5 - - - +
28E ARG 3.8 6.1 - - - +
29E THR* 3.7 15.5 - - - +
30E TRP* 3.5 33.4 - - + +
62E VAL* 4.3 11.9 - - + -
104E PHE* 4.1 16.6 - - + +
105E GLN 4.3 2.2 - - - -
106E LEU* 4.0 34.8 - - + +
111E GLY* 4.2 0.5 - - - -
112E PRO* 3.3 5.5 - - - +
113E VAL* 2.7 37.3 + - + +
115E LEU* 3.7 27.1 - - + -
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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