Contacts of the strand formed by residues 29 - 36 (chain C) in PDB entry 2EWY
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 GLY 29 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLN 4.0 0.2 - - - +
24C GLY* 3.4 6.9 - - - -
25C ASP* 2.9 30.1 + - - +
26C SER* 4.3 2.9 + - - -
27C GLY 3.6 0.8 - - - -
28C ARG* 1.3 81.4 - - - +
30C TYR* 1.3 65.1 + - - -
31C TYR* 4.1 7.2 - - - -
46C LEU* 4.0 12.6 - - - -
131C TRP* 5.0 0.6 - - - -
245C THR* 5.0 1.9 + - - -
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Residues in contact with TYR 30 (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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22C LEU* 4.2 17.3 - - + -
23C GLN 3.3 7.2 - - - +
24C GLY 3.6 18.2 - - - -
25C ASP* 3.5 21.3 - - - -
26C SER* 3.6 6.8 + - - -
29C GLY* 1.3 78.3 - - - -
31C TYR* 1.3 61.0 + - - +
46C LEU* 3.2 7.1 - - - +
47C VAL* 2.9 31.3 + - + +
168C MET* 5.7 2.2 - - - -
170C MET* 3.2 48.1 - - + +
171C CYS 3.3 11.3 + - - -
184C GLY 3.5 30.5 - - - -
185C GLY* 4.4 4.3 - - - -
242C SER 5.8 2.0 - - - -
347C ALA* 5.2 1.8 - - + -
351C GLU* 2.6 29.0 + - - -
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Residues in contact with TYR 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ASN 4.1 0.5 - - - +
22C LEU* 3.5 7.1 - - - -
23C GLN* 2.7 84.0 + - + +
24C GLY* 3.9 7.8 + - - -
29C GLY 4.1 7.2 - - - -
30C TYR* 1.3 77.0 - - - +
32C LEU* 1.3 57.9 + - - +
33C GLU 4.2 0.3 + - - -
44C GLN* 3.7 33.4 - - + -
45C ILE 2.9 22.9 - - - +
46C LEU* 4.0 1.1 - - - -
130C LYS* 3.3 49.6 + - + +
131C TRP* 4.0 23.3 - + + -
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Residues in contact with LEU 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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21C ASN* 3.5 42.8 - - + +
22C LEU* 3.7 13.0 - - + +
31C TYR* 1.3 74.0 - - - +
33C GLU* 1.3 68.4 + - - +
34C MET* 3.5 28.7 - - + -
44C GLN* 3.6 3.2 - - - -
45C ILE* 2.6 46.6 + - + +
47C VAL* 4.1 7.5 - - + +
103C ILE* 4.0 28.3 - - + -
135C LEU* 4.4 4.5 - - + -
187C LEU* 4.0 18.4 - - + -
189C LEU* 5.0 0.9 - - + -
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Residues in contact with GLU 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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21C ASN 4.5 3.4 + - - +
31C TYR* 4.2 1.0 + - - -
32C LEU* 1.3 83.1 - - - +
34C MET* 1.3 64.1 + - - +
35C LEU* 4.3 3.8 - - - +
42C LYS* 2.9 40.8 + - + +
43C LEU 3.5 12.6 - - - +
44C GLN* 3.6 18.7 + - - +
103C ILE* 4.4 2.9 - - - +
104C PRO* 3.2 38.9 - - + +
105C LYS* 6.0 6.3 - - - -
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Residues in contact with MET 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 LEU* 3.5 27.4 - - + +
33C GLU* 1.3 76.9 - - - +
35C LEU* 1.3 65.6 + - - +
36C ILE* 4.4 3.8 - - + +
41C GLN 3.8 0.5 - - - +
42C LYS* 4.0 0.3 - - - -
43C LEU* 2.9 33.4 + - - +
45C ILE* 3.3 26.7 - - + -
54C PHE* 3.2 33.7 - - + -
101C VAL* 4.0 15.3 - - + -
102C THR 3.6 10.8 - - - +
103C ILE* 4.0 9.0 - - + -
104C PRO* 3.9 1.3 - - - -
135C LEU* 4.0 14.4 - - + -
152C PHE* 3.6 23.8 - - + -
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Residues in contact with LEU 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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33C GLU* 4.3 7.2 - - - +
34C MET* 1.3 75.2 - - - +
36C ILE* 1.3 61.2 + - - +
40C PRO* 4.0 27.1 - - + -
41C GLN 3.4 2.5 - - - -
42C LYS* 3.8 35.7 - - + +
100C LEU 4.0 0.3 - - - +
101C VAL* 3.5 4.9 - - - +
102C THR* 2.8 51.7 + - + +
104C PRO* 3.8 21.5 - - + -
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Residues in contact with ILE 36 (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 MET* 4.4 8.7 - - + +
35C LEU* 1.3 79.8 - - - +
37C GLY* 1.3 68.1 + - - +
39C PRO 3.6 1.0 - - - +
41C GLN* 2.8 47.2 + - - +
43C LEU* 3.2 34.3 - - + -
45C ILE* 5.2 0.4 - - + -
54C PHE* 4.1 16.6 - - + -
56C VAL* 4.0 14.4 - - + -
68C PHE* 3.5 30.3 - - + -
99C ASP* 4.6 5.4 - - + -
100C LEU 3.8 7.0 - - - +
101C VAL* 4.7 12.1 - - + -
115C ILE* 4.1 14.1 - - + -
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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