Contacts of the helix formed by residues 56 - 65 (chain G) in PDB entry 5M64
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 56 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1662A ASN* 3.4 11.4 - - - +
53G TYR* 3.1 30.9 - - - +
54G LEU 3.1 1.2 - - - -
55G GLU* 1.3 107.2 + - - +
57G PRO* 1.3 64.3 - - - +
58G LEU* 3.3 3.6 - - + -
59G GLN* 2.5 42.7 + - + +
60G GLY 2.9 20.6 + - - -
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Residues in contact with PRO 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1660A VAL* 3.7 22.2 - - + -
1662A ASN* 3.2 23.3 - - - +
49G LEU* 3.8 27.2 - - + +
53G TYR* 3.2 9.2 - - + +
54G LEU* 3.4 18.6 - - + +
56G ASN* 1.3 86.5 - - - +
58G LEU* 1.3 61.2 + - - +
60G GLY* 3.3 1.4 + - - +
61G VAL* 3.1 26.6 + - - +
89G ILE* 5.0 7.6 - - + -
103G LYS* 4.3 13.5 - - + +
105G ILE* 5.5 3.6 - - + -
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Residues in contact with LEU 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1662A ASN* 3.5 21.8 - - + +
1663A ALA 3.5 33.4 - - - +
56G ASN* 5.5 0.9 - - + -
57G PRO* 1.3 79.7 - - - +
59G GLN* 1.3 77.1 + - + +
61G VAL* 3.4 10.2 - - - +
62G MET* 3.1 31.9 + - + +
87G LEU* 5.1 25.3 - - + +
89G ILE* 6.1 2.9 - - + -
103G LYS* 4.6 6.5 - - - +
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Residues in contact with GLN 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G TYR* 4.8 7.8 - - + -
56G ASN* 2.5 44.4 + - + +
58G LEU* 1.3 87.5 - - + +
60G GLY* 1.3 59.0 + - - +
62G MET* 3.3 24.3 + - + +
63G LYS* 2.9 50.1 + - - +
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Residues in contact with GLY 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G LEU* 5.6 1.6 - - - -
50G ALA* 6.1 2.2 - - - -
53G TYR* 3.6 37.6 - - - +
56G ASN 2.9 10.1 + - - -
57G PRO 3.3 3.1 + - - -
59G GLN* 1.3 76.5 - - - +
61G VAL* 1.3 57.3 + - - +
63G LYS* 3.1 5.0 + - - +
64G GLN* 3.0 30.7 + - - +
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Residues in contact with VAL 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G LEU* 4.8 6.7 - - + -
47G VAL* 3.6 29.6 - - + -
48G SER 4.7 1.3 - - - +
49G LEU* 4.4 14.5 - - + +
57G PRO 3.1 18.8 + - - +
58G LEU* 3.4 13.5 - - - +
60G GLY* 1.3 74.7 - - - +
62G MET* 1.3 61.2 + - - +
65G HIS* 2.9 46.6 + - + +
66G LEU* 3.1 12.0 + - + +
87G LEU* 6.5 0.9 - - + -
116G THR* 6.2 0.9 - - + -
118G CYS* 5.7 8.3 - - - -
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Residues in contact with MET 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D GLU* 5.5 7.0 - - - +
58G LEU* 3.1 26.4 + - + +
59G GLN* 3.5 30.5 - - + +
60G GLY 3.1 0.2 - - - -
61G VAL* 1.3 79.2 - - + +
63G LYS* 1.3 69.8 + - - +
66G LEU* 3.3 20.1 - - + +
67G ASN* 3.0 37.9 + - - +
84G TYR* 3.5 27.8 - - - +
87G LEU* 4.3 17.9 - - + -
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Residues in contact with LYS 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A VAL* 5.1 12.6 - - + +
571A HIS* 6.3 1.3 - - + -
82D LEU* 5.6 3.6 - - + -
53G TYR* 4.6 21.1 - - + +
59G GLN* 2.9 45.3 + - - +
60G GLY* 3.1 6.2 + - - +
62G MET* 1.3 95.2 - - - +
64G GLN* 1.3 60.0 + - + +
67G ASN* 3.3 21.8 + - - +
68G PRO* 3.8 14.7 - - - +
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Residues in contact with GLN 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A VAL 2.9 28.6 + - - +
569A SER* 3.6 3.1 - - - -
571A HIS* 4.2 5.3 - - - +
572A THR* 3.6 30.5 + - + +
16D LEU* 3.4 35.3 - - + +
17D ASN* 2.9 27.2 - - - +
53G TYR* 6.3 1.1 - - + -
60G GLY 3.0 14.7 + - - +
63G LYS* 1.3 79.4 - - + +
65G HIS* 1.3 70.5 + - + +
66G LEU 3.6 0.7 - - - -
68G PRO* 3.6 17.8 - - - +
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Residues in contact with HIS 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D THR 4.1 9.8 + - - -
16D LEU* 2.7 40.7 + - - +
17D ASN 2.6 26.9 + - - +
18D THR 4.0 5.6 + - - -
19D PRO* 4.0 12.5 - - + +
45G LEU* 5.3 7.5 - - + +
47G VAL* 3.3 31.2 - - + +
48G SER* 4.6 12.5 + - - -
49G LEU* 6.3 0.2 - - - -
61G VAL* 2.9 26.9 + - + +
64G GLN* 1.3 88.2 - - + +
66G LEU* 1.3 61.1 + - - +
68G PRO* 4.7 1.6 - - - -
69G LEU* 3.5 20.9 - - - +
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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