Contacts of the helix formed by residues 46 - 60 (chain A) in PDB entry 3D5K
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 ASP 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PHE 3.3 1.7 - - - +
45A ARG* 1.3 75.7 - - - +
47A PRO* 1.4 65.9 - - - +
48A GLN* 2.9 21.5 + - - +
49A LEU* 3.2 19.8 + - + +
50A GLN* 3.1 28.6 + - - +
165A TYR* 2.9 30.4 + - + -
169A LYS* 5.1 0.2 - - - +
249A GLY* 3.4 4.7 - - - -
250A LEU* 3.3 37.7 + - + +
256A LEU* 4.2 11.8 + - + +
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Residues in contact with PRO 47 (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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45A ARG 3.3 9.8 - - - +
46A ASP* 1.4 88.5 - - - +
48A GLN* 1.3 62.0 + - - -
50A GLN* 3.7 18.2 - - - +
51A GLN* 3.2 17.8 + - - +
247A PRO* 3.7 24.3 - - + +
248A GLN 3.4 20.9 - - - +
250A LEU* 4.7 9.6 - - + -
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Residues in contact with GLN 48 (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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46A ASP* 2.9 11.9 + - - +
47A PRO* 1.3 78.3 - - - +
49A LEU* 1.3 62.1 + - - +
51A GLN 3.7 0.5 + - - -
52A LEU* 3.2 23.8 + - + +
165A TYR* 3.2 33.4 + - + +
169A LYS* 5.2 4.8 - - - +
246A LEU* 3.7 33.6 - - + +
247A PRO* 2.9 39.7 - - - +
248A GLN* 4.8 0.2 - - - -
249A GLY* 4.0 11.7 + - - -
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Residues in contact with LEU 49 (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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44A PHE* 3.6 33.0 - - + -
46A ASP* 3.2 20.5 + - + +
48A GLN* 1.3 75.6 - - - +
50A GLN* 1.3 59.7 + - - +
52A LEU* 3.3 6.5 + - + -
53A ILE* 2.9 51.2 + - + +
161A VAL* 4.2 7.6 - - + -
162A ALA* 3.9 22.0 - - + +
165A TYR* 3.8 46.6 - - + -
166A LEU* 5.3 7.2 - - + -
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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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40A TRP* 3.6 19.1 - - + -
41A ARG* 2.8 64.8 + - - +
44A PHE* 2.7 31.1 + - + +
45A ARG* 4.1 7.9 + - - +
46A ASP 3.1 13.3 + - - +
47A PRO* 3.7 17.6 - - - +
48A GLN 3.4 0.4 - - - -
49A LEU* 1.3 74.7 - - - +
51A GLN* 1.3 63.0 + - - +
53A ILE* 4.7 0.9 - - - -
54A GLY* 3.2 18.2 + - - -
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Residues in contact with GLN 51 (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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41A ARG* 4.8 2.2 - - - +
47A PRO 3.2 13.8 + - - +
48A GLN 4.1 4.3 - - - +
49A LEU 3.3 0.2 - - - -
50A GLN* 1.3 77.4 - - - +
52A LEU* 1.3 58.0 - - - +
54A GLY* 3.4 2.2 + - - -
55A VAL* 3.0 39.9 + - + +
243A PRO* 4.2 17.0 - - - +
245A ASN* 4.5 12.0 + - - +
246A LEU* 3.9 24.3 - - + +
247A PRO* 3.2 27.9 - - + +
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Residues in contact with LEU 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 GLN* 3.2 18.3 + - + +
49A LEU* 3.3 8.2 + - - +
51A GLN* 1.3 76.1 - - - +
53A ILE* 1.3 59.7 + - - +
55A VAL* 3.2 4.9 + - + +
56A ALA* 2.9 23.7 + - - +
161A VAL* 4.5 7.0 - - + -
165A TYR* 3.5 37.9 - - + -
234A LEU* 4.4 13.2 - - + -
238A LEU* 3.4 43.3 - - + +
242A ILE* 4.7 5.4 - - + -
243A PRO* 4.1 13.0 - - + -
246A LEU* 4.0 23.1 - - + -
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Residues in contact with ILE 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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40A TRP* 3.9 34.5 - - + -
44A PHE* 3.7 37.0 - - + -
49A LEU* 2.9 39.0 + - + +
50A GLN* 4.8 0.2 - - - -
52A LEU* 1.3 71.9 - - - +
54A GLY* 1.3 57.8 + - - +
56A ALA* 3.2 7.3 + - + +
57A LEU* 2.9 33.7 + - + +
158A VAL* 4.1 29.8 - - + +
161A VAL* 3.9 21.5 - - + -
162A ALA* 5.2 0.2 - - + -
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Residues in contact with GLY 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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40A TRP* 4.2 11.3 - - - -
41A ARG* 5.9 1.8 - - - -
50A GLN 3.2 15.3 + - - -
51A GLN* 3.7 4.0 - - - -
53A ILE* 1.3 76.7 - - - +
55A VAL* 1.3 61.8 + - - +
57A LEU* 3.5 14.0 + - - +
58A GLU* 3.6 15.1 + - - +
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Residues in contact with VAL 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 GLN* 3.0 26.4 + - + +
52A LEU* 3.5 10.5 - - - +
54A GLY* 1.3 74.8 - - - +
56A ALA* 1.3 57.2 + - - +
58A GLU* 3.4 5.0 + - - +
59A ASN* 3.0 50.2 + - - +
238A LEU* 4.1 23.8 - - + +
240A SER* 4.2 14.1 - - - +
241A GLY 4.9 3.6 - - - +
243A PRO* 4.4 20.6 - - + -
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Residues in contact with ALA 56 (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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52A LEU 2.9 16.1 + - - +
53A ILE* 3.2 6.0 + - + +
55A VAL* 1.3 76.1 - - - +
57A LEU* 1.3 60.7 + - + +
60A ASN* 3.0 32.6 + - - +
63A LEU* 5.1 0.3 - - - +
157A LEU* 3.6 9.5 - - + +
161A VAL* 3.7 29.4 - - + -
237A LEU 3.9 11.7 - - - +
238A LEU* 3.7 15.7 - - + +
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Residues in contact with LEU 57 (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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40A TRP* 3.5 36.1 - - + +
53A ILE* 2.9 22.5 + - + +
54A GLY* 3.9 7.4 - - - +
55A VAL 3.3 0.4 - - - -
56A ALA* 1.3 76.9 - - + +
58A GLU* 1.3 58.8 + - + +
60A ASN 5.0 0.9 - - - +
63A LEU* 3.8 26.5 - - + +
154A GLN* 3.6 32.3 - - + +
157A LEU* 4.5 7.4 - - + -
158A VAL* 4.3 10.3 - - + -
476A NA 3.9 15.5 - - - -
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Residues in contact with GLU 58 (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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54A GLY 3.6 10.9 + - - +
55A VAL* 3.6 6.6 - - - +
56A ALA 3.1 0.4 - - - -
57A LEU* 1.3 81.5 - - + +
59A ASN* 1.3 75.2 + - - +
60A ASN 3.8 1.3 - - - -
64A ARG* 2.7 32.6 + - - -
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Residues in contact with ASN 59 (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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55A VAL* 3.0 31.9 + - - +
58A GLU* 1.3 102.8 + - - +
60A ASN* 1.3 62.7 + - - +
61A ARG* 2.7 32.2 + - - -
64A ARG* 4.0 8.8 + - - +
238A LEU 3.1 19.1 - - - +
239A GLY* 3.6 14.5 - - - +
240A SER* 4.0 12.8 + - - -
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Residues in contact with ASN 60 (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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56A ALA 3.0 20.7 + - - +
57A LEU 5.5 0.9 - - - +
58A GLU 5.2 1.4 - - - +
59A ASN* 1.3 75.7 - - - +
61A ARG* 1.3 63.3 + - - +
62A ASP* 2.9 33.0 + - - +
63A LEU* 3.1 13.6 + - + +
64A ARG* 3.3 19.4 + - - +
157A LEU* 3.4 27.6 - - + +
236A LEU 4.2 4.4 + - - -
237A LEU* 2.9 36.1 + - - +
238A LEU 3.6 5.1 + - - -
239A GLY* 4.3 4.3 - - - -
360B LYS* 6.4 0.2 - - - +
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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