Contacts of the strand formed by residues 52 - 57 (chain H) in PDB entry 4NL3
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 52 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65G SER* 3.1 24.5 - - - +
66G PRO 3.8 19.3 - - - +
67G GLN* 5.8 2.9 - - - +
69G ASN* 3.8 7.4 - - - +
47H LEU 3.6 0.3 - - - +
48H ASP* 3.7 1.7 - - - -
49H VAL* 2.8 42.7 + - - +
50H GLU 3.1 3.7 + - - +
51H GLY* 1.3 78.9 - - - +
53H GLN* 1.3 85.9 + - - +
54H GLN* 3.8 8.7 + - - +
1L MET 4.4 15.6 - - - +
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Residues in contact with GLN 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G TYR* 2.5 41.4 + - - +
66G PRO* 3.2 22.9 - - + +
69G ASN* 3.3 26.8 + - - +
70G VAL 2.9 43.0 + - - +
72G LEU* 3.3 20.4 - - - +
38H VAL* 5.5 4.9 - - + +
46H LEU* 4.2 11.2 - - + +
47H LEU 3.4 6.1 - - - +
48H ASP* 5.5 3.1 - - - +
52H LYS* 1.3 78.3 - - - +
54H GLN* 1.3 68.2 + - - +
55H LEU 4.2 0.2 - - - -
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Residues in contact with GLN 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PHE* 5.2 0.2 - - - -
63G THR* 3.5 24.9 - - + +
64G PHE 3.6 2.0 - - - +
65G SER* 2.7 29.5 + - - -
33H LEU* 3.5 21.8 - - + -
45H VAL 3.5 0.7 - - - +
46H LEU* 3.7 3.5 - - - +
47H LEU* 2.9 47.4 + - + +
49H VAL* 3.6 26.6 - - + +
52H LYS* 3.8 12.5 + - - +
53H GLN* 1.3 84.3 + - - +
55H LEU* 1.3 62.7 + - - +
56H VAL* 3.4 7.2 + - + +
1L MET 4.3 14.1 + - - +
2L LYS* 5.1 2.8 - - + +
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Residues in contact with LEU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LEU* 3.9 18.8 - - + -
9G GLN* 5.0 4.3 - - + +
12G TYR* 3.5 40.6 + - + -
13G LEU* 4.5 11.9 - - + -
63G THR* 3.3 3.3 - - - -
64G PHE* 2.6 67.5 + - + +
44H THR* 3.8 33.7 - - + -
45H VAL 4.2 3.6 - - - +
46H LEU* 4.1 14.0 - - + +
53H GLN 4.2 0.4 - - - -
54H GLN* 1.3 69.1 - - - +
56H VAL* 1.3 62.0 + - - +
57H PHE* 4.1 3.5 + - + -
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Residues in contact with VAL 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G SER 3.7 11.2 - - - +
63G THR* 4.2 10.5 - - + +
25H VAL* 5.3 0.4 - - + -
27H LEU* 4.1 15.5 - - + -
33H LEU* 5.0 5.8 - - + -
44H THR* 3.2 4.3 - - - -
45H VAL* 2.8 40.9 + - - +
47H LEU* 3.6 28.3 - - + -
54H GLN* 3.7 15.5 - - + +
55H LEU* 1.3 76.3 - - - +
57H PHE* 1.3 66.2 + - - +
60H ALA* 5.0 0.2 - - + -
61H ILE* 3.5 33.9 - - + -
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Residues in contact with PHE 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G GLN* 3.4 30.1 - - + -
13G LEU* 4.9 2.7 - - + -
45G VAL* 5.7 0.2 - - + -
58G LYS* 4.0 21.3 - - + -
61G ILE* 3.7 25.6 - - + +
62G SER 3.2 11.2 + - - +
64G PHE* 3.7 32.8 - + - -
43H PHE 3.6 5.8 - - - -
44H THR* 4.0 16.6 - - + -
55H LEU* 4.6 6.1 - - + -
56H VAL* 1.3 75.3 - - - +
58H LYS* 1.3 60.2 + - - +
59H HIS* 3.3 37.2 - + + +
60H ALA* 2.9 24.6 + - - +
61H ILE* 3.5 6.8 + - - +
21R U 3.4 13.5 - - - -
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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