Contacts of the helix formed by residues 48 - 55 (chain A) in PDB entry 1EG4
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 ALA 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A PRO* 1.3 70.7 - - - +
49A SER* 1.3 63.0 + - - +
50A GLN 2.9 1.7 + - - -
51A HIS* 3.0 33.3 + - + +
52A PHE* 4.1 1.2 + - - +
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 3.2 8.5 + - - +
48A ALA* 1.3 75.6 - - - +
50A GLN* 1.3 58.7 + - - +
52A PHE* 3.0 14.2 + - - +
53A LEU* 2.8 36.3 + - - +
63A ARG* 4.9 4.0 + - - -
65A ILE* 5.8 1.9 - - - +
148A LEU* 4.6 13.5 - - - +
151A ILE* 3.8 34.2 - - - +
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Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PRO* 3.1 19.3 + - + +
48A ALA 2.9 1.2 + - - -
49A SER* 1.3 75.3 + - - +
51A HIS* 1.3 74.6 + - + +
53A LEU 4.5 0.2 - - - +
54A SER* 2.9 32.3 + - - -
63A ARG* 2.6 65.7 + - - +
64A ALA* 4.0 5.7 - - - +
65A ILE* 3.4 31.2 - - + +
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Residues in contact with HIS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO 5.9 0.9 - - - -
48A ALA* 3.0 22.7 + - + +
50A GLN* 1.3 82.0 - - + +
52A PHE* 1.3 65.4 + - - +
54A SER* 3.1 15.0 + - - -
55A THR* 4.5 4.3 + - - +
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA 4.1 0.8 + - - +
49A SER* 3.0 14.3 + - - +
51A HIS* 1.3 83.5 - - - +
53A LEU* 1.3 83.4 + - + +
55A THR* 3.3 17.7 + - - +
151A ILE* 5.3 4.5 - - + -
155A THR* 3.6 32.1 - - + -
159A ASP* 5.6 1.1 - - - -
171A VAL* 4.0 23.1 - - + -
172A PRO* 3.7 29.1 - - + +
175A VAL* 4.7 1.3 - - + -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A SER* 2.8 21.0 + - - +
52A PHE* 1.3 96.9 - - + +
54A SER* 1.3 64.0 + - - +
55A THR 3.1 3.4 - - - -
56A SER* 3.1 23.7 + - - -
63A ARG* 3.3 40.9 - - - +
151A ILE* 3.7 35.9 - - + -
172A PRO* 3.7 27.8 - - + +
175A VAL* 3.9 14.8 - - + -
176A ASP* 4.1 9.2 - - - +
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN* 2.9 26.4 + - - -
51A HIS* 3.1 14.7 + - - -
53A LEU* 1.3 77.4 - - - +
55A THR* 1.3 63.4 + - - +
56A SER 3.3 3.8 + - - -
57A VAL* 3.5 22.5 + - - +
63A ARG* 4.0 17.4 + - - +
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A HIS 4.7 2.9 - - - +
52A PHE 3.3 17.2 + - - +
54A SER* 1.3 80.4 + - - +
56A SER* 1.3 58.3 + - - +
57A VAL 3.1 13.1 + - - +
58A GLN* 3.8 9.9 + - - -
170A ASN* 5.7 2.3 + - - -
172A PRO* 3.6 18.0 - - - +
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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