Contacts of the helix formed by residues 50 - 59 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B TYR* 2.8 38.6 + - + +
49B PRO* 1.3 69.7 - - - +
51B PRO* 1.3 73.9 - - + +
53B ILE* 3.0 19.2 + - + +
54B ARG* 3.0 38.9 + - + +
172B LYS* 6.1 0.9 - - + -
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Residues in contact with PRO 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B TYR* 3.6 23.6 - - + +
48B TYR 4.7 1.3 - - - +
49B PRO* 3.4 4.7 - - + -
50B VAL* 1.3 95.9 - - + +
52B LEU* 1.3 61.4 + - + +
54B ARG* 3.2 24.5 - - - +
55B ARG* 2.9 30.2 + - - +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.5 21.9 - - + -
34B GLU* 3.9 28.5 - - + +
35B ILE* 4.0 19.3 - - + -
38B VAL* 4.0 22.7 - - + -
39B ALA* 6.2 0.7 - - - -
42B TYR* 4.9 4.0 - - + -
49B PRO* 3.3 14.5 + - + +
50B VAL 3.3 0.6 - - - -
51B PRO* 1.3 84.7 - - + +
53B ILE* 1.3 56.1 + - + +
55B ARG* 3.0 6.6 + - + +
56B ALA* 2.8 36.8 + - - +
94B VAL* 4.0 28.5 - - + -
98B ILE* 5.7 3.1 - - + -
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 4.9 8.1 - - + -
49B PRO* 3.2 24.7 - - + +
50B VAL* 3.0 12.6 + - + +
52B LEU* 1.3 78.2 - - + +
54B ARG* 1.3 59.2 + - + +
56B ALA* 3.5 5.4 + - - +
57B TRP* 3.0 24.6 + - - +
62B MET* 3.8 12.5 - - + +
94B VAL* 4.5 3.1 - - + +
97B ALA* 4.1 14.4 - - + -
98B ILE* 3.7 25.4 - - + -
128B PRO* 5.1 7.6 - - + +
130B MET* 3.6 46.0 - - + -
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Residues in contact with ARG 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 3.0 32.8 + - + +
51B PRO* 3.2 28.6 - - - +
53B ILE* 1.3 74.7 - - + +
55B ARG* 1.3 58.9 + - + +
57B TRP* 3.1 10.0 + - + +
58B GLU* 2.7 53.5 + - + +
128B PRO* 4.3 21.9 - - + +
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LYS* 4.9 8.3 - - - +
30B PHE* 3.7 12.3 - - + -
34B GLU* 3.2 30.8 + - - +
51B PRO 2.9 15.6 + - - +
52B LEU* 3.4 10.3 - - + +
54B ARG* 1.3 79.5 - - + +
56B ALA* 1.3 57.0 + - - +
58B GLU* 3.2 35.4 + - - +
59B LEU* 2.8 72.6 + - - +
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.9 20.1 - - + -
52B LEU 2.8 16.3 + - - +
53B ILE 3.7 4.5 - - - +
55B ARG* 1.3 74.1 - - - +
57B TRP* 1.3 58.3 + - - +
59B LEU* 2.9 6.3 + - - +
60B GLY 2.7 32.1 + - - -
61B LEU* 3.1 21.2 + - + -
62B MET* 4.4 7.6 - - + -
87B LEU* 5.6 0.2 - - + -
98B ILE* 4.1 20.0 - - + -
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Residues in contact with TRP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ILE 3.0 16.5 + - - +
54B ARG* 3.2 16.2 - - + +
56B ALA* 1.3 76.3 - - - +
58B GLU* 1.3 77.2 + - + +
60B GLY* 3.7 7.5 + - - -
62B MET* 4.1 27.9 - - + +
63B ASN* 4.7 4.7 - - + -
124B MET 2.8 24.1 + - - -
125B THR 3.3 22.9 + - - -
126B GLU 3.4 26.0 - - - -
127B GLU* 3.1 10.2 + - - -
128B PRO* 3.6 31.9 - - + -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ARG* 2.7 49.7 + - + +
55B ARG* 3.2 38.3 + - - +
56B ALA 3.0 0.2 - - - -
57B TRP* 1.3 91.4 - - + +
59B LEU* 1.3 63.3 + - - +
60B GLY* 3.1 1.6 + - - -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR* 4.3 17.4 - - + +
29B LYS* 6.3 0.4 - - - +
30B PHE* 3.7 36.3 - - + -
34B GLU* 4.7 1.3 - - - +
55B ARG* 2.8 58.1 + - - +
56B ALA* 2.9 3.5 + - - +
58B GLU* 1.3 76.6 - - - +
60B GLY* 1.3 60.7 + - - +
61B LEU* 3.4 20.3 + - + +
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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