Contacts of the helix formed by residues 60 - 70 (chain A) in PDB entry 2XMS
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 ASN 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A HIS* 3.6 12.1 - - - -
59A LEU* 1.3 75.0 - - - +
61A TYR* 1.3 64.8 + - - +
62A LYS* 2.9 9.4 + - - +
63A SER* 2.8 33.3 + - - -
64A CYS* 2.9 23.9 + - - +
87A ASP* 3.4 12.3 - - - +
91A MET* 3.9 15.9 + - + +
1307A IMD 3.1 29.8 + - + -
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Residues in contact with TYR 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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39A THR* 3.4 30.3 - - - +
41A TYR* 2.6 38.0 + + - -
53A THR* 4.6 4.9 - - - +
55A HIS* 3.7 10.5 - - - -
60A ASN* 1.3 72.3 - - - +
62A LYS* 1.3 71.8 + - + +
65A PHE* 2.8 36.1 + - + +
66A GLN 3.8 0.7 + - - -
85A HIS* 3.4 31.9 - + + -
86A VAL 3.9 11.2 - - - +
87A ASP* 2.9 35.2 + - - +
1306A IMD 3.6 20.6 - + - -
1307A IMD 3.3 23.6 - + - -
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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
----------------------------------------------------------
41A TYR* 4.0 12.0 + - - -
60A ASN* 2.9 10.2 + - - +
61A TYR* 1.3 102.2 - - + +
63A SER* 1.3 62.7 + - - +
64A CYS 3.1 1.3 - - - -
66A GLN* 2.8 64.2 + - - +
67A PRO* 4.1 1.9 - - - +
70A GLN* 3.9 6.1 + - - -
1306A IMD 3.1 26.4 - - - +
1307A IMD 4.0 16.8 - - + -
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.3 11.9 - - - +
60A ASN* 2.8 42.5 + - - -
62A LYS* 1.3 74.1 - - - +
64A CYS* 1.3 59.2 + - - +
67A PRO* 4.7 0.8 - - - +
203A TYR* 2.6 46.6 + - - -
206A ILE* 4.4 18.8 - - - +
283A LEU* 3.5 6.8 - - - +
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Residues in contact with CYS 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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55A HIS* 3.5 16.6 - - + -
56A ASP 3.7 19.1 - - - -
59A LEU* 3.6 17.3 - - + -
60A ASN 2.9 18.9 + - - +
63A SER* 1.3 80.2 + - - +
65A PHE* 1.3 63.7 + - + +
66A GLN 3.9 0.2 - - - -
67A PRO* 4.6 0.2 - - - +
131A VAL* 3.6 31.0 - - - -
282A GLN* 3.1 37.7 - - - +
283A LEU* 3.6 7.1 - - - +
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A THR* 3.5 25.8 - - - -
54A TYR 3.6 30.7 - - - -
55A HIS* 3.7 7.9 - - - -
61A TYR* 2.8 27.8 + - - +
64A CYS* 1.3 81.0 - - + +
66A GLN* 1.3 60.2 + - - +
67A PRO* 3.5 2.7 - - - -
68A LEU* 3.3 12.7 + - + +
69A PHE* 2.9 55.3 + + + +
85A HIS* 4.6 1.6 - - - +
129A VAL* 3.7 30.5 - - + -
131A VAL* 3.8 29.2 - - + -
155A ILE* 5.0 1.1 - - + -
282A GLN* 4.6 4.0 - - + -
1306A IMD 3.8 8.1 - - + -
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Residues in contact with GLN 66 (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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62A LYS* 2.8 51.1 + - - +
65A PHE* 1.3 76.8 - - - +
67A PRO* 1.3 71.1 - - + +
70A GLN* 2.9 60.9 + - - +
1306A IMD 3.4 20.2 + - + -
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Residues in contact with PRO 67 (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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62A LYS 4.1 4.0 - - - +
63A SER 4.7 1.3 - - - +
64A CYS 4.6 0.2 - - - +
65A PHE 3.7 2.7 - - - -
66A GLN* 1.3 98.7 - - + +
68A LEU* 1.3 59.7 + - - +
70A GLN* 4.1 1.5 - - + -
71A PHE* 3.2 22.7 + - - +
199A LEU* 6.2 2.5 - - + -
202A LYS* 6.3 1.3 - - - +
203A TYR* 4.8 4.7 - - - +
282A GLN 4.1 11.7 - - - +
283A LEU* 3.8 37.2 - - + +
286A PRO* 3.7 13.0 - - + +
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Residues in contact with LEU 68 (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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65A PHE* 3.3 15.4 + - + +
66A GLN 3.2 0.6 - - - -
67A PRO* 1.3 78.9 - - - +
69A PHE* 1.3 85.7 + - + +
71A PHE* 3.1 13.3 + - - +
74A MET* 3.2 46.2 - - + +
129A VAL* 4.9 9.9 - - + -
282A GLN* 3.9 20.7 + - + +
286A PRO* 3.7 17.7 - - + +
289A LEU* 4.0 32.8 - - + -
290A THR* 3.6 15.3 - - - +
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Residues in contact with PHE 69 (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 ILE* 4.0 22.7 - - + -
53A THR* 3.5 30.3 - - + -
65A PHE* 2.9 38.6 + + + +
68A LEU* 1.3 97.2 - - + +
70A GLN* 1.3 60.0 + - - +
71A PHE 3.5 0.4 + - - -
74A MET* 3.9 11.6 - - + +
75A GLN* 3.7 8.8 - - - +
78A ILE* 3.2 42.0 - - + +
83A ARG* 4.3 8.1 - - + -
85A HIS* 3.8 16.4 - + - -
129A VAL* 4.8 7.2 - - + -
293A PHE* 6.1 1.6 - + - -
1305A CL 3.8 13.2 - - + -
1306A IMD 3.7 19.2 - - + +
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 3.9 8.3 + - - -
66A GLN* 2.9 53.0 + - + +
67A PRO* 4.1 2.2 - - + +
69A PHE* 1.3 76.7 - - - +
71A PHE* 1.3 67.9 + - - +
72A GLU* 3.4 2.4 + - - -
75A GLN* 3.9 22.0 + - - +
1306A IMD 4.3 11.6 - - + -
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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