Contacts of the strand formed by residues 61 - 66 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K VAL* 3.8 24.2 - - + -
26K PHE 3.9 2.7 - - - -
27K LEU* 4.4 1.3 - - + +
28K THR* 4.0 1.2 + - - -
45K VAL* 4.0 26.9 - - + -
47K LEU* 6.4 0.2 - - + -
56K VAL* 3.5 26.0 - - + -
57K PHE 3.5 11.0 - - - +
58K LYS* 3.0 17.4 + - - +
60K ALA* 1.3 79.4 - - - +
62K SER* 1.3 62.2 + - - +
63K THR 4.1 6.1 - - - +
64K PHE* 3.8 19.7 - - + -
57L PHE* 3.6 24.1 - - + -
59L HIS* 2.8 32.4 + - - -
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Residues in contact with SER 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K PHE* 2.8 20.2 + - - +
27K LEU 4.0 15.3 - - - -
28K THR* 4.1 7.2 - - - -
60K ALA 3.7 0.4 + - - -
61K ILE* 1.3 76.3 - - - +
63K THR* 1.3 69.5 + - - +
27L LEU* 3.5 15.9 - - - +
29L ASN* 4.0 7.9 + - - -
56L VAL* 3.5 4.5 - - - +
57L PHE* 3.0 26.6 + - - -
60L ALA* 3.5 21.6 - - - +
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Residues in contact with THR 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K THR 3.6 0.9 - - - +
25K VAL* 3.6 6.9 - - - +
26K PHE* 3.1 39.0 + - + +
61K ILE* 4.1 0.8 - - - +
62K SER* 1.3 92.0 + - - +
64K PHE* 1.3 67.9 + - - +
65K SER* 4.0 9.0 - - - +
27L LEU* 3.9 10.6 - - - +
33L LEU* 4.6 4.1 - - + +
54L GLN* 3.7 31.2 - - + +
55L LEU 3.3 10.1 - - - +
56L VAL* 3.8 16.7 - - + +
57L PHE* 5.3 0.2 - - - -
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Residues in contact with PHE 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K TYR* 4.9 0.9 - - + -
13K LEU* 3.8 30.1 - - + -
16K LEU* 4.2 18.8 - - + -
23K ALA* 4.4 7.9 - - + -
24K THR 3.8 0.9 - - - -
25K VAL* 3.4 31.9 - - + -
37K VAL* 4.3 14.8 - - + -
45K VAL* 4.5 14.1 - - + -
47K LEU* 4.9 1.1 - - + -
61K ILE* 3.8 24.0 - - + -
63K THR* 1.3 71.5 - - - +
65K SER* 1.3 60.6 + - - +
66K PRO* 3.4 8.3 - - - +
54L GLN* 3.7 2.9 - - - -
55L LEU* 2.6 49.5 + - + +
57L PHE* 3.7 31.2 - + - -
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Residues in contact with SER 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K ALA* 3.3 2.1 - - - -
24K THR* 2.5 56.2 + - - +
26K PHE* 4.3 11.2 - - - -
63K THR* 4.0 5.8 - - - +
64K PHE* 1.3 71.2 - - - +
66K PRO* 1.3 62.4 - - - +
67K GLN* 4.1 0.3 + - - +
52L LYS* 6.5 0.7 - - - -
53L GLN 4.5 0.2 - - - -
54L GLN* 3.3 33.8 + - - +
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Residues in contact with PRO 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K TYR* 3.2 24.2 - - + +
16K LEU* 4.0 13.7 - - + -
21K ILE* 3.5 12.6 - - + -
22K LEU 3.6 7.0 - - - +
23K ALA* 3.8 4.5 - - + -
64K PHE 3.4 8.3 - - - +
65K SER* 1.3 86.3 - - - +
67K GLN* 1.3 55.0 + - - +
68K LYS 3.4 21.1 - - - +
52L LYS* 2.6 32.8 + - + +
53L GLN* 3.3 23.8 - - + +
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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