Contacts of the strand formed by residues 30 - 35 (chain C) in PDB entry 1EAW
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 GLN 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C TRP* 2.9 26.6 + - + +
28C PRO 4.3 4.5 - - - +
29C TRP* 1.3 86.2 - - + +
31C VAL* 1.3 85.9 + - - +
43C GLY* 3.9 6.5 - - - -
44C ALA 3.7 11.2 + - - +
67C PHE 4.4 3.5 - - - +
68C LEU* 4.9 0.3 - - - -
69C GLY 4.7 8.1 + - - -
70C LEU 5.4 1.9 + - - +
139C THR* 2.5 40.9 + - - +
140C GLY* 4.8 1.4 - - - -
141C TRP* 3.6 33.3 - - + -
155C LEU* 4.1 13.2 - - + -
197C GLY* 4.7 0.8 - - - -
198C PRO* 3.7 15.0 - - + +
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PRO 5.6 0.7 - - - +
29C TRP 3.1 19.1 - - - +
30C GLN* 1.3 83.5 + - - +
32C SER* 1.3 63.6 + - - +
33C LEU* 5.1 0.2 - - + -
43C GLY* 3.1 7.1 - - - -
44C ALA* 2.6 48.3 + - + +
46C LEU* 4.0 3.6 - - + +
52C LEU* 3.8 27.6 - - + -
66C ALA* 3.8 18.2 - - + -
67C PHE 3.2 16.4 - - - +
68C LEU* 3.2 25.4 - - + -
141C TRP* 4.1 1.6 - - - -
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Residues in contact with SER 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 1.3 72.6 - - - +
33C LEU* 1.3 61.9 + - - +
34C HIS* 3.2 22.2 + - - -
40C HIS* 3.5 7.8 + - - -
42C CYS 4.2 1.8 - - - -
43C GLY* 4.7 0.4 - - - -
65C THR 3.7 0.3 - - - +
66C ALA* 3.1 4.3 - - - +
67C PHE* 2.7 41.0 + - - +
70C LEU* 3.6 26.0 - - - -
73C GLN* 3.4 10.2 + - - -
141C TRP* 3.6 19.8 - - - -
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 5.1 0.4 - - + -
32C SER* 1.3 75.2 + - - +
34C HIS* 1.3 64.2 + - - +
40C HIS* 4.3 0.2 + - - -
41C ILE 3.2 22.7 + - - -
42C CYS 2.9 22.0 + - - +
43C GLY 4.3 2.2 - - - +
44C ALA* 3.6 20.6 - - + -
52C LEU* 5.1 0.9 - - + -
59C TYR* 2.9 30.3 - - + +
64C TRP* 4.0 16.8 - - + -
65C THR 3.3 19.7 - - - +
66C ALA* 3.5 20.6 - - + +
85C LEU* 4.0 20.4 - - + -
106C LEU* 3.2 19.1 - - + -
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Residues in contact with HIS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C SER* 3.2 20.2 + - - -
33C LEU* 1.3 74.7 - - - +
35C ALA* 1.3 60.5 + - - +
39C GLY* 3.2 13.9 - - - -
40C HIS* 2.9 27.1 + - + -
64C TRP* 3.4 5.9 - - - -
65C THR* 2.5 48.1 + - - +
67C PHE* 3.4 35.3 - + + -
70C LEU* 4.3 1.4 - - - +
73C GLN* 3.2 27.1 + - - -
76C ARG* 3.9 22.6 + - - -
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Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C HIS* 1.3 77.0 - - - +
36C LEU* 1.3 61.2 + - - +
37C GLY 3.3 0.3 + - - -
38C GLN* 2.8 29.4 + - + -
39C GLY* 3.0 13.1 + - - -
41C ILE* 3.6 27.6 - - + +
60C ARG* 4.7 9.6 - - - +
63C GLN 3.6 7.4 - - - +
64C TRP* 4.1 17.5 - - + -
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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