Contacts of the helix formed by residues 48 - 53 (chain D) in PDB entry 3E2A
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 PRO 48 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D SER 4.7 3.6 - - - +
46D ARG 3.3 7.8 - - - +
47D VAL* 1.3 91.3 - - + +
49D ALA* 1.3 65.3 + - - +
50D GLU* 3.9 6.7 - - - +
51D LYS* 3.0 34.3 + - + +
52D LEU* 3.1 11.3 + - - +
64D ARG* 4.7 3.6 - - - +
48F PRO* 3.9 28.3 - - + -
50F GLU* 3.7 27.6 - - + +
51F LYS 5.8 0.2 - - - +
57F PRO* 4.9 7.0 - - + -
232F BCT 4.0 8.7 - - - +
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TRP* 3.4 44.9 - - + +
45D SER* 6.3 0.2 - - - -
47D VAL 3.5 2.4 + - - -
48D PRO* 1.3 70.3 - - - +
50D GLU* 1.3 60.4 + - - +
52D LEU* 3.9 12.8 - - - -
53D THR* 2.4 42.3 + - - +
60D LEU* 3.9 9.2 - - + -
62D VAL* 5.1 5.4 - - + -
64D ARG* 5.5 3.2 - - - +
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D PRO* 3.9 3.6 - - - +
49D ALA* 1.3 88.1 + - - +
51D LYS* 1.3 61.7 + - - +
53D THR* 3.8 4.7 + - - -
54D ASN* 3.5 14.9 + - - -
55D LEU* 4.1 8.4 + - - +
57D PRO* 6.1 2.7 - - + -
58D GLY 6.0 3.4 - - - +
60D LEU* 4.1 15.5 - - + +
62D VAL* 3.8 12.1 - - - +
45F SER 4.5 5.0 - - - +
46F ARG* 4.3 13.9 - - - +
48F PRO* 3.6 31.3 - - + +
64F ARG* 2.6 40.8 + - - -
232F BCT 4.3 0.9 - - - +
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Residues in contact with LYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D VAL* 4.0 12.6 - - + -
48D PRO* 3.0 29.1 + - + +
50D GLU* 1.3 77.2 - - - +
52D LEU* 1.3 65.9 + - - +
54D ASN* 3.2 14.4 + - - -
14F TRP* 3.7 41.5 + - + +
18F MET* 5.3 9.3 - - - +
48F PRO* 5.1 1.5 - - + +
51F LYS* 5.9 7.4 - - - +
57F PRO* 5.6 9.0 - - + -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TRP* 4.0 9.2 - - + -
47D VAL* 3.6 29.6 - - + +
48D PRO 3.1 7.9 + - - +
49D ALA* 3.6 13.5 - - - +
51D LYS* 1.3 79.2 - - - +
53D THR* 1.3 78.2 + - + +
54D ASN 3.6 0.3 + - - -
181D PHE* 3.9 31.2 - - + -
188D LEU* 3.8 31.4 - - + -
11F ASN* 3.1 28.2 + - - +
14F TRP* 3.6 29.6 - - + +
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Residues in contact with THR 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TRP* 3.5 32.3 - - + -
49D ALA 2.4 29.6 + - - +
50D GLU* 3.8 3.8 + - - -
52D LEU* 1.3 83.5 - - + +
54D ASN* 1.3 75.2 + - - +
55D LEU* 3.3 22.1 + - - +
60D LEU* 3.5 13.0 - - + +
7F LEU* 3.8 23.5 - - + +
10F ASN* 3.2 14.2 - - - +
11F ASN* 3.8 7.4 + - - +
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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