Contacts of the helix formed by residues 50 - 59 (chain C) in PDB entry 1EGE
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 VAL 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C TYR* 2.9 40.1 + - + +
49C PRO* 1.3 70.8 - - - +
51C PRO* 1.3 72.0 - - + +
53C ILE* 3.2 18.5 + - + +
54C ARG* 3.2 36.9 + - + +
172C LYS* 5.6 3.6 - - + +
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Residues in contact with PRO 51 (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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42C TYR* 3.2 25.8 - - + +
48C TYR 4.4 1.8 - - - +
49C PRO* 3.4 0.7 - - + -
50C VAL* 1.3 98.2 - - + +
52C LEU* 1.3 64.0 + - + +
54C ARG* 3.7 6.3 + - + +
55C ARG* 3.3 18.9 + - - +
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Residues in contact with LEU 52 (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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30C PHE* 3.7 21.7 - - + -
34C GLU* 3.6 31.2 - - + +
35C ILE* 4.1 10.8 - - + +
38C VAL* 3.3 27.8 - - + -
39C ALA 5.1 0.2 - - - +
42C TYR* 4.0 16.2 - - + +
49C PRO* 2.9 9.4 + - + +
51C PRO* 1.3 78.1 - - + +
53C ILE* 1.3 64.9 + - - +
55C ARG* 3.3 6.9 + - + +
56C ALA* 3.1 19.2 + - - +
94C VAL* 3.9 40.2 - - + -
98C ILE* 5.3 0.6 - - - +
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Residues in contact with ILE 53 (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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48C TYR* 3.6 41.7 - - + +
49C PRO* 3.0 31.6 + - + +
50C VAL* 3.2 8.7 + - + +
52C LEU* 1.3 73.4 - - + +
54C ARG* 1.3 71.4 + - + +
56C ALA* 3.1 5.7 + - - +
57C TRP* 3.0 20.3 + - - +
62C MET* 3.9 21.3 - - + +
94C VAL* 5.3 1.8 - - + +
97C ALA* 4.6 4.7 - - + -
98C ILE* 4.4 18.2 - - + -
128C PRO* 5.2 6.3 - - + +
130C MET* 3.7 22.0 - - + -
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Residues in contact with ARG 54 (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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50C VAL* 3.2 33.0 + - + +
51C PRO* 4.1 5.6 - - - +
53C ILE* 1.3 79.4 - - + +
55C ARG* 1.3 57.2 + - - +
57C TRP* 3.2 13.7 + - + +
58C GLU* 2.8 33.0 + - - +
128C PRO* 3.4 41.2 + - + +
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Residues in contact with ARG 55 (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 LYS* 4.4 9.3 - - - +
30C PHE* 3.5 13.2 - - + -
34C GLU* 3.1 39.5 + - - +
51C PRO 3.3 12.4 + - - +
52C LEU* 3.3 13.2 + - + +
53C ILE 3.1 0.6 - - - -
54C ARG* 1.3 78.3 - - - +
56C ALA* 1.3 61.7 + - - +
58C GLU* 3.0 37.6 + - - +
59C LEU* 3.0 53.9 + - - +
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Residues in contact with ALA 56 (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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30C PHE* 4.1 13.2 - - + -
52C LEU 3.1 10.2 + - - +
53C ILE 3.1 9.4 + - - +
55C ARG* 1.3 72.1 - - - +
57C TRP* 1.3 69.0 + - - +
59C LEU* 2.8 16.9 + - - +
60C GLY 3.0 8.3 + - - -
61C LEU* 3.2 36.3 + - + -
62C MET* 4.5 3.6 - - + -
87C LEU* 4.8 0.7 - - + -
98C ILE* 4.1 20.4 - - + -
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Residues in contact with TRP 57 (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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53C ILE 3.0 12.1 + - - +
54C ARG* 3.4 10.5 - - + +
56C ALA* 1.3 75.4 - - - +
58C GLU* 1.3 74.4 + - + +
60C GLY* 3.1 14.0 + - - -
61C LEU 4.8 0.4 - - - +
62C MET* 4.1 24.0 - - + +
63C ASN* 3.5 21.2 - - - +
124C MET 2.9 19.2 + - - -
125C THR* 3.4 23.2 + - - +
126C GLU 3.9 10.5 - - - -
127C GLU 3.5 15.5 - - - -
128C PRO* 3.6 46.0 - - + +
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Residues in contact with GLU 58 (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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54C ARG* 2.8 15.6 + - - +
55C ARG* 3.0 39.7 + - - +
57C TRP* 1.3 85.1 - - + +
59C LEU* 1.3 58.3 + - + +
60C GLY* 2.9 9.5 + - - -
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Residues in contact with LEU 59 (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 THR* 4.6 13.3 - - + +
29C LYS* 4.1 15.7 - - - +
30C PHE* 3.5 46.7 - - + -
34C GLU* 5.8 0.2 - - - -
55C ARG* 3.0 50.0 - - - +
56C ALA* 2.8 6.7 + - - +
58C GLU* 1.3 76.9 - - + +
60C GLY* 1.3 63.5 + - - +
61C LEU* 3.7 17.8 + - + +
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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