Contacts of the helix formed by residues 61 - 71 (chain A) in PDB entry 4F2N
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 LYS 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLU* 4.4 9.0 - - - +
57A LEU* 3.0 31.3 + - + +
60A SER* 1.3 90.0 - - - +
62A HIS* 1.3 66.7 + - - +
63A HIS 3.5 0.2 - - - -
64A SER* 3.6 1.1 + - - -
65A ALA* 3.0 26.7 + - - +
203B ASN* 3.9 40.6 - - + +
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Residues in contact with HIS 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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57A LEU 3.1 24.8 + - - -
58A HIS* 3.3 20.0 - - + +
61A LYS* 1.3 83.0 - - - +
63A HIS* 1.3 64.2 + - - +
65A ALA* 3.2 9.8 + - - +
66A TYR* 3.2 27.2 + - + -
108A HIS* 5.0 0.2 - - - +
195A HIS* 3.4 43.5 + + + +
194B GLU* 3.6 8.9 + - - -
197B TYR* 6.1 0.2 - - - -
198B TYR* 2.6 32.3 + + - -
203B ASN* 3.5 25.2 - - + +
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Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 3.4 12.1 - - + +
36A PRO* 3.4 18.5 - - + +
58A HIS 2.9 16.9 + - - +
59A TYR* 3.5 15.2 + - - +
62A HIS* 1.3 71.7 - - - +
64A SER* 1.3 63.8 + - - +
66A TYR* 3.1 20.0 + - + +
67A VAL* 3.1 9.2 + - + +
104A GLN 4.7 0.2 - - - -
105A HIS* 3.0 39.1 + - - -
108A HIS* 3.5 18.1 - + + +
109A SER* 3.3 28.0 + - - -
112A TRP* 2.9 26.9 + - + +
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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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35A LEU* 3.6 24.5 - - - +
59A TYR 3.1 9.7 + - - -
60A SER* 3.2 31.3 + - - -
61A LYS 3.9 0.7 - - - -
62A HIS 3.3 0.2 - - - -
63A HIS* 1.3 75.3 - - - +
65A ALA* 1.3 57.3 + - - +
67A VAL* 3.4 2.3 + - - +
68A ASP* 3.0 41.8 + - - +
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Residues in contact with ALA 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 LYS 3.0 18.9 + - - +
62A HIS* 3.2 5.1 + - - +
64A SER* 1.3 73.0 - - - +
66A TYR* 1.3 62.4 + - + +
68A ASP* 3.8 7.6 - - - +
69A LYS* 2.8 33.0 + - - +
101A GLN* 4.6 0.7 - - - -
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Residues in contact with TYR 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 HIS* 3.2 32.2 + - + -
63A HIS* 3.1 12.4 + + - +
65A ALA* 1.3 78.3 - - + +
67A VAL* 1.3 56.8 + - - +
70A LEU* 2.9 33.1 + - - +
101A GLN* 3.3 39.3 - - - +
104A GLN* 3.1 44.0 + - + -
105A HIS* 4.4 8.5 - - - +
108A HIS* 3.6 25.8 - + - -
193A TRP* 3.6 21.0 - - - -
195A HIS* 4.6 3.9 - + - -
152B PHE* 4.1 14.2 - + - -
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Residues in contact with VAL 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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33A ALA* 3.6 34.7 - - - +
34A GLU* 3.9 6.1 - - - +
35A LEU* 4.0 19.5 - - + +
63A HIS* 3.1 17.8 + - + +
64A SER* 3.6 9.0 - - - +
65A ALA 3.3 0.2 - - - -
66A TYR* 1.3 77.4 - - - +
68A ASP* 1.3 69.9 + - - +
70A LEU* 3.3 2.7 + - - +
71A ASN* 3.0 28.5 + - - +
105A HIS* 3.7 34.5 - - + +
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Residues in contact with ASP 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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64A SER* 3.0 27.7 + - - +
65A ALA* 3.8 7.4 - - - +
67A VAL* 1.3 81.9 - - - +
69A LYS* 1.3 62.5 + - - +
71A ASN* 3.3 17.1 + - - +
72A THR* 3.4 16.4 + - - +
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Residues in contact with LYS 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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65A ALA 2.8 22.1 + - - +
68A ASP* 1.3 74.2 - - - +
70A LEU* 1.3 62.7 + - - +
72A THR* 2.6 37.7 + - + +
73A LEU* 3.6 13.9 + - + +
97A VAL* 4.4 17.9 - - - -
101A GLN* 3.3 30.5 - - + +
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Residues in contact with LEU 70 (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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31A TYR* 3.5 17.0 + - + -
33A ALA* 3.8 22.0 - - + -
66A TYR 2.9 19.1 + - - +
67A VAL 3.6 3.8 - - - +
69A LYS* 1.3 76.4 - - - +
71A ASN* 1.3 58.1 + - - +
72A THR 3.1 0.2 - - - -
73A LEU* 2.9 19.5 + - - +
74A GLY 2.9 13.3 + - - -
82A ILE* 4.0 17.9 - - + -
85A ILE* 4.6 6.3 - - + -
98A MET* 4.0 28.0 - - + +
101A GLN* 3.8 11.4 - - + +
102A ALA* 3.9 33.0 - - + +
105A HIS* 4.2 8.5 - - + -
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Residues in contact with ASN 71 (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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31A TYR* 3.4 22.3 + - - +
32A PRO* 3.7 8.9 - - - +
33A ALA* 2.9 45.9 + - - +
67A VAL* 3.0 23.2 + - - +
68A ASP* 3.6 12.7 + - - +
69A LYS 3.2 0.4 - - - -
70A LEU* 1.3 76.7 - - - +
72A THR* 1.3 58.5 + - + +
73A LEU 3.3 0.4 - - - -
75A LYS 5.6 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