Contacts of the strand formed by residues 23 - 27 (chain G) 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 ALA 23 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16G LEU* 4.7 9.0 - - + -
21G ILE 3.8 3.8 + - - +
22G LEU* 1.3 79.5 - - - +
24G THR* 1.3 62.4 + - - +
25G VAL* 3.8 4.1 + - + +
33G LEU 3.7 1.0 - - - +
34G ARG* 3.5 4.1 - - - -
35G GLY 3.1 36.0 + - - +
37G VAL* 5.8 3.6 - - + -
64G PHE* 4.5 20.2 - - + -
65G SER 3.2 13.2 - - - +
66G PRO* 3.8 12.3 - - + -
67G GLN 4.4 0.2 - - - +
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Residues in contact with THR 24 (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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23G ALA* 1.3 72.9 - - - +
25G VAL* 1.3 62.1 + - - +
26G PHE* 3.6 33.1 + - + -
32G GLN* 4.3 23.6 - - + +
33G LEU 3.5 8.7 - - - +
34G ARG* 2.6 40.0 + - + +
64G PHE* 4.0 0.2 - - - -
65G SER* 2.6 39.9 + - - -
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Residues in contact with VAL 25 (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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23G ALA* 4.5 7.0 - - + +
24G THR* 1.3 74.3 - - - +
26G PHE* 1.3 61.3 + - - +
27G LEU* 3.6 17.0 + - + +
32G GLN* 3.4 4.1 - - - -
33G LEU* 2.6 44.4 + - + +
35G GLY 5.7 2.5 - - - +
47G LEU* 3.9 28.7 - - + -
56G VAL* 5.2 0.2 - - + -
61G ILE* 3.8 32.8 - - + -
63G THR 3.7 4.7 - - - +
64G PHE* 3.5 30.5 - - + -
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Residues in contact with PHE 26 (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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24G THR* 3.8 21.8 - - + -
25G VAL* 1.3 71.0 - - - +
27G LEU* 1.3 64.8 + - - +
30G GLY 5.4 4.0 - - - -
31G PHE 4.1 3.4 - - - -
32G GLN* 3.1 30.7 - - + -
61G ILE* 3.8 2.4 - - - +
62G SER* 2.7 28.0 + - - -
63G THR* 3.0 34.6 + - - +
65G SER* 3.8 24.2 - - - -
31H PHE* 5.8 5.6 - + - -
2L LYS* 3.9 43.1 - - + -
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Residues in contact with LEU 27 (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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25G VAL* 4.1 18.2 - - + +
26G PHE* 1.3 84.0 - - - +
28G THR* 1.3 65.7 + - - +
29G ASN* 3.2 22.9 - - - +
30G GLY* 3.3 10.9 + - - -
31G PHE* 2.9 28.1 + - + +
32G GLN* 4.8 1.1 - - - +
33G LEU* 4.6 12.6 - - + -
56G VAL* 4.0 23.3 - - + -
60G ALA* 3.3 13.7 - - + +
61G ILE* 4.4 1.8 - - - -
62G SER* 4.0 3.0 - - - -
29H ASN* 3.9 6.8 + - - -
26J PHE* 6.4 0.7 - - + -
62J SER* 3.5 21.8 - - - +
63J THR* 3.9 14.1 - - + -
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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