Contacts of the strand formed by residues 61 - 66 (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 ILE 61 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 3.8 18.8 - - + -
26C PHE 4.1 2.2 - - - -
27C LEU* 4.4 1.6 - - + -
28C THR* 4.1 1.0 + - - -
45C VAL* 3.8 30.7 - - + -
47C LEU* 6.0 0.7 - - + -
56C VAL* 3.6 24.0 - - + -
57C PHE 3.4 10.8 - - - +
58C LYS* 3.0 18.5 + - + +
60C ALA* 1.3 79.0 - - - +
62C SER* 1.3 62.6 + - - +
63C THR 4.1 4.5 - - - +
64C PHE* 3.8 25.6 - - + -
57K PHE* 3.7 24.5 - - + +
59K HIS* 2.7 32.2 + - - -
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Residues in contact with SER 62 (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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26C PHE* 2.8 22.0 + - - +
27C LEU 4.0 14.6 - - - -
28C THR* 4.1 9.6 - - - -
60C ALA 3.7 0.2 + - - -
61C ILE* 1.3 76.3 - - - +
63C THR* 1.3 64.8 + - - +
27K LEU* 3.2 30.1 - - - +
29K ASN* 4.5 4.5 + - - -
56K VAL* 3.6 4.2 - - - +
57K PHE* 3.1 26.3 + - - +
60K ALA* 3.8 14.9 - - - +
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Residues in contact with THR 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C THR 3.9 0.3 - - - +
25C VAL* 3.7 6.6 - - - +
26C PHE* 3.1 38.3 + - + +
61C ILE* 4.5 0.7 - - - -
62C SER* 1.3 92.7 + - - +
64C PHE* 1.3 73.4 + - - +
65C SER* 3.9 2.9 - - - +
27K LEU* 4.0 9.2 - - - +
33K LEU* 4.2 4.6 - - + +
54K GLN* 3.6 34.1 - - + +
55K LEU 3.2 13.7 - - - +
56K VAL* 4.0 14.1 - - + +
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Residues in contact with PHE 64 (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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12C TYR* 4.9 1.5 + - + -
13C LEU* 3.8 31.6 - - + -
16C LEU* 4.2 19.1 - - + -
23C ALA* 4.5 7.6 - - + -
24C THR 4.1 0.4 - - - -
25C VAL* 3.5 29.2 - - + -
37C VAL* 4.4 14.4 - - + -
45C VAL* 4.3 14.1 - - + -
47C LEU* 5.0 0.7 - - + -
61C ILE* 3.8 35.9 - - + -
63C THR* 1.3 72.5 - - - +
65C SER* 1.3 61.0 + - - +
66C PRO* 3.3 9.0 - - + +
54K GLN* 3.9 2.9 - - - -
55K LEU* 2.7 49.2 + - + +
57K PHE* 3.9 23.8 - + - -
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Residues in contact with SER 65 (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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23C ALA* 3.3 1.1 - - - -
24C THR* 2.5 51.6 + - - -
26C PHE* 4.1 19.2 - - - -
63C THR* 3.9 2.0 - - - -
64C PHE* 1.3 73.7 - - - +
66C PRO* 1.3 60.1 - - - +
67C GLN 4.0 0.3 + - - -
52K LYS* 3.5 17.7 + - - -
54K GLN* 3.0 24.6 + - - -
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Residues in contact with PRO 66 (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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12C TYR* 3.3 24.5 - - + +
16C LEU* 3.9 22.2 - - + -
21C ILE* 4.2 0.4 - - + -
22C LEU 3.5 8.3 - - - +
23C ALA* 3.7 5.4 - - + -
64C PHE 3.3 12.1 - - - +
65C SER* 1.3 85.3 - - - +
67C GLN* 1.3 64.6 + - - +
68C LYS 3.4 21.5 - - - +
69C ASN* 5.0 0.4 - - - -
52K LYS* 3.1 24.4 + - - +
53K GLN* 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