Contacts of the helix formed by residues 53 - 64 (chain A) in PDB entry 2X1L
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 GLY 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A HIS* 1.3 78.7 - - - +
54A GLN* 1.3 65.4 + - - -
55A LYS 3.4 2.5 - - - -
56A MET 3.5 1.7 + - - -
57A ALA* 3.1 18.0 + - - +
131A GLU* 3.5 9.9 - - - -
213A PHE* 4.0 12.8 - - - -
215A TRP* 3.2 19.8 + - - -
229A VAL* 4.0 13.9 - - - +
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Residues in contact with GLN 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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53A GLY* 1.3 69.6 - - - -
55A LYS* 1.3 57.0 + - - +
57A ALA* 3.1 6.8 + - - +
58A GLU* 2.8 42.3 + - + +
126A TYR* 3.3 14.5 + - - -
128A ILE* 4.0 30.9 - - + +
131A GLU* 3.1 8.5 + - - +
210A ARG* 2.9 39.6 + - - +
212A THR* 5.0 2.4 + - - -
213A PHE* 3.5 39.0 - - + -
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Residues in contact with LYS 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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13A TYR* 4.4 28.1 - - + -
15A ASN* 3.8 30.3 + - + +
54A GLN* 1.3 76.3 - - - +
56A MET* 1.3 56.8 - - + +
58A GLU* 3.6 3.6 + - - +
59A THR* 2.7 37.1 + - - +
128A ILE* 3.5 23.4 - - + +
129A ARG* 3.1 44.2 + - - +
131A GLU* 3.0 16.8 + - + +
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Residues in contact with MET 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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13A TYR* 4.5 9.4 - - + -
14A PRO* 3.6 48.5 - - + +
15A ASN* 3.6 12.1 - - - -
50A ASP 4.3 4.7 - - - +
51A VAL 3.3 30.7 - - - +
52A HIS 3.7 10.3 - - - +
53A GLY 3.5 5.6 + - - +
54A GLN 3.2 0.4 - - - -
55A LYS* 1.3 76.7 - - - +
57A ALA* 1.3 59.4 + - - +
59A THR* 3.4 1.8 + - - -
60A ALA* 3.0 29.2 + - - +
67A ALA* 5.0 2.6 - - - +
70A LEU* 3.6 24.0 - - + +
71A ALA* 3.9 23.6 - - + +
215A TRP* 3.8 7.9 - - - +
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Residues in contact with ALA 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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53A GLY 3.1 15.2 + - - +
54A GLN* 3.1 8.4 + - + +
56A MET* 1.3 79.2 - - - +
58A GLU* 1.3 58.8 + - + +
60A ALA* 3.5 7.5 + - - +
61A ALA* 3.0 28.3 + - - +
67A ALA* 4.5 6.1 - - + -
213A PHE* 5.3 6.3 - - + -
215A TRP* 4.0 22.2 - - + -
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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 GLN* 2.8 24.7 + - + +
55A LYS* 3.9 4.7 - - - +
57A ALA* 1.3 71.8 - - + +
59A THR* 1.3 64.7 + - - +
61A ALA* 3.2 7.4 + - - +
62A LYS* 3.0 43.3 + - - +
128A ILE* 3.2 43.8 - - - +
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Residues in contact with THR 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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15A ASN* 3.3 40.2 + - + +
55A LYS* 2.7 24.0 + - - +
56A MET 3.6 4.9 - - - -
58A GLU* 1.3 75.9 - - - +
60A ALA* 1.3 62.8 + - - +
62A LYS* 3.4 12.2 + - + +
63A GLU* 3.2 35.8 + - + +
70A LEU* 3.9 13.0 - - + -
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Residues in contact with ALA 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 MET 3.0 17.2 + - - +
57A ALA 3.6 5.2 - - - +
59A THR* 1.3 77.2 - - - +
61A ALA* 1.3 56.6 + - - +
63A GLU* 3.3 2.6 + - - +
64A GLY 3.0 20.8 + - - -
65A ILE* 3.0 33.2 + - - +
66A PRO 4.1 1.1 - - - -
67A ALA* 3.7 25.4 - - + +
70A LEU* 3.6 17.2 - - + +
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Residues in contact with ALA 61 (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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57A ALA 3.0 17.7 + - - +
58A GLU* 3.2 8.0 + - - +
60A ALA* 1.3 76.3 - - - +
62A LYS* 1.3 63.9 + - + +
64A GLY* 3.3 12.3 + - - +
65A ILE 4.7 1.6 - - - +
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Residues in contact with LYS 62 (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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58A GLU* 3.0 35.0 + - - +
59A THR* 3.7 10.1 - - + +
60A ALA 3.3 0.2 - - - -
61A ALA* 1.3 77.4 - - + +
63A GLU* 1.3 62.1 + - + +
64A GLY* 3.6 0.3 + - - -
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Residues in contact with GLU 63 (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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15A ASN 4.9 2.9 - - - +
59A THR* 3.2 23.0 + - + +
60A ALA 3.3 4.7 + - - +
62A LYS* 1.3 77.9 - - + +
64A GLY* 1.3 61.8 + - - +
65A ILE* 3.4 12.5 + - + +
70A LEU* 3.5 17.1 - - - +
73A ARG* 2.9 38.1 + - - -
74A ASN* 5.2 0.7 + - - -
305C SER* 3.9 14.6 + - - -
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Residues in contact with GLY 64 (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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60A ALA 3.0 5.1 + - - -
61A ALA* 3.3 9.6 + - - -
62A LYS 3.3 4.0 + - - -
63A GLU* 1.3 78.8 - - - +
65A ILE* 1.3 63.7 + - - +
66A PRO* 4.8 0.9 - - - +
305C SER* 3.8 14.3 + - - +
342C GLU* 5.1 5.3 - - - +
346C ILE* 6.3 1.8 - - - -
512C TYR* 4.4 19.1 + - - -
513C GLN 5.3 2.1 - - - +
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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