Contacts of the helix formed by residues 22 - 32 (chain C) in PDB entry 3E6C
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 ILE 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C PHE* 3.8 11.9 - - + +
21C PRO* 1.3 76.4 - - - +
23C GLU* 1.3 59.9 + - - +
24C LYS* 4.1 4.9 - - + +
25C LEU* 3.3 32.4 + - + +
55C PHE* 3.4 17.6 - - + -
81C ASN* 2.9 13.3 + - - +
83C LEU* 4.1 12.6 - - + -
122C MET* 4.2 9.2 - - - -
125C GLU* 3.5 58.1 - - + +
126C ILE* 4.0 15.9 - - + +
129C ASN* 4.0 14.4 - - + +
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Residues in contact with GLU 23 (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 PRO* 3.8 3.8 + - + -
22C ILE* 1.3 73.9 - - - +
24C LYS* 1.3 70.1 + - - +
26C ARG* 2.7 48.0 - - - +
27C ASN* 4.6 3.7 + - - +
81C ASN* 3.7 25.4 - - - +
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Residues in contact with LYS 24 (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 ILE* 3.2 5.0 - - + +
23C GLU* 1.3 89.3 - - + +
25C LEU* 1.3 58.9 + - - +
26C ARG 3.1 1.1 - - - -
27C ASN* 3.1 46.2 + - - +
28C TYR* 3.5 9.4 + - + -
119C ASP* 4.7 9.1 + - - -
122C MET* 3.7 29.2 - - + -
125C GLU* 5.9 3.1 - - + -
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Residues in contact with LEU 25 (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 ILE* 3.3 35.3 + - + +
23C GLU 3.2 1.6 - - - -
24C LYS* 1.3 74.0 - - - +
26C ARG* 1.3 63.4 + - - +
27C ASN 3.2 0.7 - - - -
28C TYR* 3.2 25.5 + - + -
29C THR* 3.6 12.6 + - - +
55C PHE* 3.8 31.2 - - + -
83C LEU* 4.0 20.0 - - + -
107C PHE* 3.9 24.9 - - + -
112C LEU* 5.4 5.4 - - + -
115C VAL* 4.5 14.4 - - + -
122C MET* 4.4 10.1 - - + -
126C ILE* 5.0 9.6 - - + -
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Residues in contact with ARG 26 (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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23C GLU* 2.7 44.8 + - - +
25C LEU* 1.3 79.2 - - - +
27C ASN* 1.3 60.0 + - - +
28C TYR 3.2 2.0 + - - -
29C THR* 3.5 19.4 + - + -
30C GLN* 4.9 0.7 - - - +
55C PHE* 3.9 12.5 - - + -
57C VAL* 2.5 52.1 + - + +
58C GLU* 4.8 6.1 + - - -
80C GLY* 5.1 0.4 - - - -
81C ASN* 2.8 32.1 + - - +
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Residues in contact with ASN 27 (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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23C GLU* 4.9 4.1 + - - +
24C LYS* 3.1 49.9 + - - +
26C ARG* 1.3 76.6 - - - +
28C TYR* 1.3 75.3 + - + +
30C GLN* 3.1 21.3 + - - +
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Residues in contact with TYR 28 (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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24C LYS* 3.5 26.3 + - + -
25C LEU* 3.2 18.4 + - + +
27C ASN* 1.3 97.7 + - + +
29C THR* 1.3 64.2 + - - +
30C GLN* 3.2 9.4 - - - +
31C MET* 3.1 33.4 + - + +
107C PHE* 3.4 12.4 - - - -
115C VAL* 4.1 23.6 - - + -
118C THR* 3.9 23.9 - - + +
119C ASP* 2.6 39.9 + - + +
122C MET* 3.8 17.9 - - + -
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Residues in contact with THR 29 (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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25C LEU 3.7 14.6 - - - +
26C ARG* 3.5 14.9 + - + +
28C TYR* 1.3 77.7 - - - +
30C GLN* 1.3 60.5 + - - +
32C GLY 2.9 26.2 + - - +
34C ILE* 4.2 17.1 - - - +
55C PHE* 3.9 17.7 - - + -
57C VAL* 4.3 8.1 - - + -
105C CYS* 3.6 34.7 - - + -
107C PHE* 4.0 1.8 - - + -
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Residues in contact with GLN 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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26C ARG 4.9 0.5 - - - +
27C ASN 3.1 29.5 + - - +
28C TYR* 3.7 8.8 - - - +
29C THR* 1.3 77.9 + - - +
31C MET* 1.3 78.1 + - + +
32C GLY 3.2 5.9 + - - +
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Residues in contact with MET 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 TYR* 3.1 23.6 + - + +
30C GLN* 1.3 96.7 - - + +
32C GLY* 1.3 59.2 + - - +
107C PHE* 4.3 0.2 - - - -
111C SER* 2.9 23.2 + - - +
114C THR* 4.1 22.2 - - + -
115C VAL* 3.9 39.7 - - + -
118C THR* 3.6 29.8 - - + +
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Residues in contact with GLY 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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29C THR 2.9 17.8 + - - +
30C GLN* 4.1 5.4 - - - +
31C MET* 1.3 83.7 - - - +
33C LEU* 1.3 72.0 + - - +
34C ILE* 4.2 0.7 + - - +
105C CYS* 3.9 2.2 - - - -
106C TRP 3.5 12.1 - - - -
107C PHE* 3.8 11.7 - - - -
111C SER* 3.8 7.0 - - - -
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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