Contacts of the helix formed by residues 57 - 65 (chain A) in PDB entry 6M17
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 ARG 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LEU 5.4 0.9 - - - -
53A GLY* 4.0 13.7 - - - +
56A TRP* 1.3 82.5 - - + +
58A PHE* 1.3 65.6 + - - +
60A TYR* 4.2 10.1 - - + -
61A LEU* 3.3 39.3 + - + +
128A TYR* 4.3 4.8 + - - -
273A ALA* 4.6 9.9 + - - +
274A GLN* 3.9 22.8 + - - +
277A PHE* 4.0 36.2 - - - -
486A ASP* 3.0 36.7 + - - +
487A SER* 4.5 11.5 + - - +
490A GLY* 3.7 23.4 + - - -
491A SER* 4.8 3.2 - - - +
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Residues in contact with PHE 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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53A GLY 3.6 15.7 + - - +
54A ASN* 3.9 12.3 - - - +
57A ARG* 1.3 79.5 - - - +
59A PRO* 1.3 66.7 - - + +
61A LEU* 3.2 4.9 + - - +
62A CYS* 2.9 37.0 + - + +
70A PHE* 4.3 16.6 - + - -
71A MET* 3.6 39.9 - - + -
74A PHE* 3.7 40.6 - + + -
274A GLN* 4.1 20.2 - - + -
314A SER* 4.2 23.6 - - - -
318A ALA* 4.4 13.5 - - + -
322A TYR* 6.2 0.4 - + - -
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Residues in contact with PRO 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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54A ASN 4.0 8.1 - - - +
55A VAL 3.4 28.9 - - - +
56A TRP 4.2 0.9 - - - +
57A ARG 4.1 0.4 - - - -
58A PHE* 1.3 92.1 - - + +
60A TYR* 1.3 64.2 + - - +
62A CYS* 3.4 8.7 + - + -
63A GLN* 3.5 13.5 + - - +
318A ALA* 5.6 2.9 - - - -
321A VAL* 3.7 20.9 - - + -
322A TYR* 3.2 40.6 + - + +
325A ILE* 5.3 0.4 - - + -
393A VAL* 4.9 2.9 - - + +
398A LEU* 3.7 14.6 - - + -
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Residues in contact with TYR 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 TRP 3.4 20.8 + - - +
57A ARG* 4.2 7.4 - - + +
58A PHE 3.3 0.2 - - - -
59A PRO* 1.3 80.5 - - - +
61A LEU* 1.3 82.1 + - + +
63A GLN* 4.2 4.8 + - - +
64A SER* 3.4 20.3 + - - -
393A VAL* 3.4 30.4 + - - +
394A GLU* 3.6 18.4 - - + +
395A GLY* 4.2 19.1 - - - -
398A LEU* 5.0 2.3 - - + +
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Residues in contact with LEU 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 ARG* 3.3 30.8 + - + +
58A PHE 3.2 2.2 + - - +
60A TYR* 1.3 101.5 - - + +
62A CYS* 1.3 62.2 + - - +
63A GLN 3.4 0.4 - - - -
64A SER* 3.8 3.4 + - - -
65A HIS* 3.4 32.1 + - - +
70A PHE* 3.7 20.7 - - + -
270A ASP* 3.8 46.2 - - + +
274A GLN* 4.1 14.6 - - - +
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Residues in contact with CYS 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 PHE* 2.9 22.0 + - + +
59A PRO* 3.4 3.1 + - + -
60A TYR 3.4 0.6 - - - -
61A LEU* 1.3 78.0 - - - +
63A GLN* 1.3 65.1 + - - +
65A HIS 3.8 6.9 + - - +
67A GLY 2.9 37.5 + - - +
68A GLY* 4.1 9.0 - - - -
70A PHE* 3.9 21.6 - - + +
71A MET* 4.4 10.1 - - - -
254A LEU* 3.7 26.7 - - - -
322A TYR* 3.7 10.5 - - + +
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Residues in contact with GLN 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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59A PRO 3.5 8.3 + - - +
60A TYR* 4.2 3.5 + - - +
61A LEU 3.4 0.2 - - - -
62A CYS* 1.3 76.5 - - - +
64A SER* 1.3 64.7 - - - +
67A GLY* 3.1 23.3 + - - -
253A PHE* 4.4 11.4 - - + -
322A TYR* 3.2 23.7 + - + +
325A ILE* 4.0 23.4 - - - +
389A LEU 4.3 14.2 + - - -
390A SER* 4.9 3.8 - - - +
391A GLU 3.2 26.6 + - - +
393A VAL* 3.3 29.9 + - - +
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Residues in contact with SER 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 TYR* 3.4 19.5 + - - -
61A LEU* 3.8 6.1 + - - -
62A CYS 3.4 0.2 - - - -
63A GLN* 1.3 78.6 - - - +
65A HIS* 1.3 74.1 + - - +
66A GLY 3.1 6.3 + - - -
261A GLU* 4.0 10.2 - - - +
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Residues in contact with HIS 65 (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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61A LEU* 3.4 26.1 + - + +
62A CYS 4.1 2.0 - - - -
63A GLN 3.3 1.2 - - - -
64A SER* 1.3 87.1 + - - +
66A GLY* 1.3 57.9 + - - +
67A GLY 3.6 1.1 - - - -
69A ALA* 3.3 26.5 + - - +
70A PHE* 3.4 30.7 + + + +
261A GLU* 3.5 13.4 + - - +
266A ASP* 3.8 21.9 + - + -
267A THR* 3.3 25.8 + - - +
270A ASP* 2.5 35.0 + - + +
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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