Contacts of the strand formed by residues 52 - 57 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LEU 3.7 0.3 - - - +
48C ASP* 3.7 1.9 - - - -
49C VAL* 2.8 44.2 + - + +
50C GLU 3.1 4.1 - - - +
51C GLY* 1.3 80.4 - - - +
53C GLN* 1.3 67.0 + - - +
54C GLN* 4.5 7.6 - - - +
65F SER* 5.5 4.3 - - - +
66F PRO 3.3 15.8 + - - +
67F GLN* 2.9 28.8 + - - +
68F LYS* 4.4 1.0 - - - +
69F ASN* 3.7 15.2 + - - +
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Residues in contact with GLN 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C VAL* 5.7 4.9 - - + +
46C LEU* 4.2 13.0 - - + +
47C LEU 3.4 5.4 - - - +
48C ASP* 5.0 3.4 - - + +
52C LYS* 1.3 75.5 - - - +
54C GLN* 1.3 69.1 + - - +
55C LEU 4.3 0.2 - - - -
12F TYR* 3.0 29.6 + - - +
65F SER* 4.6 0.2 + - - -
66F PRO* 3.3 23.6 - - + +
69F ASN* 3.1 31.9 + - - +
70F VAL* 2.7 45.7 + - - +
72F LEU* 3.9 19.6 - - - +
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Residues in contact with GLN 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 3.9 29.4 - - + +
45C VAL 3.3 4.9 - - - +
46C LEU* 3.5 3.7 - - - +
47C LEU* 2.8 49.9 + - + +
49C VAL* 4.1 12.4 - - + +
52C LYS* 4.0 12.6 - - - +
53C GLN* 1.3 86.6 - - - +
55C LEU* 1.3 61.3 + - - +
56C VAL* 3.4 3.1 + - + +
26F PHE* 5.6 2.2 - - - -
63F THR* 3.6 23.1 - - + +
64F PHE 3.8 1.1 - - - -
65F SER* 3.0 33.9 + - - -
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C THR* 3.8 24.0 - - + -
45C VAL 4.1 5.8 - - - +
46C LEU* 4.0 9.9 - - + +
53C GLN 4.3 0.4 - - - -
54C GLN* 1.3 69.5 - - - +
56C VAL* 1.3 60.8 + - - +
57C PHE* 4.1 3.0 + - + -
8F LEU* 3.7 31.0 - - + -
9F GLN* 4.8 3.8 - - + -
12F TYR* 3.5 42.0 + - + -
13F LEU* 4.5 11.9 - - + -
63F THR* 3.3 2.3 - - - -
64F PHE* 2.6 65.7 + - + +
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Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 5.3 0.2 - - + -
27C LEU* 3.9 18.2 - - + -
33C LEU* 3.8 16.4 - - + -
44C THR* 3.3 3.4 - - - -
45C VAL* 2.7 41.7 + - + +
47C LEU* 3.6 29.2 - - + -
54C GLN 3.8 6.5 - - - +
55C LEU* 1.3 76.5 - - - +
57C PHE* 1.3 66.5 + - - +
60C ALA* 4.7 0.7 - - + -
61C ILE* 3.6 31.0 - - + -
62F SER 3.6 11.7 - - - +
63F THR* 3.9 8.3 - - + +
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Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PHE 3.5 5.8 - - - -
44C THR* 3.8 14.6 - - + +
55C LEU* 4.8 4.0 - - + -
56C VAL* 1.3 73.2 - - - +
58C LYS* 1.3 61.0 + - - +
59C HIS* 3.3 35.9 - + + +
60C ALA* 2.9 24.1 + - - +
61C ILE* 3.3 9.0 + - - +
9F GLN* 3.6 26.0 - - - -
13F LEU* 5.1 3.4 - - + -
45F VAL* 5.7 0.2 - - + -
58F LYS* 4.2 24.7 - - + -
61F ILE* 3.5 39.7 - - + +
62F SER 3.0 11.9 + - - +
64F PHE* 3.8 23.8 - + - -
30Z U 3.7 13.2 - - - -
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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