Contacts of the strand formed by residues 47 - 50 (chain K) in PDB entry 1N13
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 ASN 47 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51G ILE* 3.5 16.7 - - + +
52G SER* 4.1 2.0 - - - -
53H PYR 3.0 15.9 - - - +
54H ILE* 2.7 47.1 + - - +
56H PRO* 4.9 0.2 - - - +
162H LEU* 3.9 10.1 - - - +
46K VAL* 1.3 72.2 - - - +
48K LEU* 1.3 61.3 + - - +
70L GLY* 2.9 26.3 + - - -
71L ALA 2.8 13.0 + - - +
72L LEU* 3.7 16.3 - - + +
73L VAL* 2.8 32.1 + - - +
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Residues in contact with LEU 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G ARG 3.9 0.2 - - - +
51G ILE* 3.5 6.1 - - - -
52G SER* 3.0 52.0 + - - +
34K PHE* 4.8 2.0 - - + -
38K LEU* 3.8 26.2 - - + -
43K ILE* 3.8 20.4 - - + +
46K VAL* 4.1 17.3 - - + +
47K ASN* 1.3 75.8 - - - +
49K ILE* 1.3 61.4 + - - +
50K ARG 3.7 1.4 + - - -
73L VAL* 3.6 3.8 - - + +
75L THR* 3.4 21.1 - - + +
77L TYR* 4.1 23.3 - - + -
157L PHE* 3.8 24.0 - - + -
161L ALA* 5.9 0.4 - - + -
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Residues in contact with ILE 49 (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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49G ILE* 3.8 30.7 - - + -
50G ARG 4.3 3.8 - - - +
51G ILE* 3.3 33.2 - - + -
74H PRO* 5.1 2.0 - - + -
8I LEU* 3.7 34.3 - - + -
49I ILE* 3.9 19.3 - - + -
47K ASN 5.1 0.2 - - - +
48K LEU* 1.3 70.6 - - - +
50K ARG* 1.3 64.3 - - - +
51K ILE* 3.3 1.0 + - - +
72L LEU* 4.2 25.1 - - + -
73L VAL 2.8 15.9 + - - +
74L PRO* 3.3 4.0 - - + +
75L THR 2.8 25.6 + - - -
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Residues in contact with ARG 50 (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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50G ARG 4.6 5.5 + - - +
52G SER* 5.0 1.1 + - - +
48I LEU 4.0 6.1 - - - +
49I ILE* 4.3 8.7 - - - +
50I ARG* 4.5 5.0 + - - +
7004J MRD 5.9 1.5 + - - -
48K LEU 3.7 4.9 + - - -
49K ILE* 1.3 75.6 - - - +
51K ILE* 1.3 69.7 + - - +
52K SER* 5.2 2.0 + - - -
75L THR 3.2 8.5 - - - +
77L TYR* 2.9 69.4 + - + +
78L GLY* 4.4 5.1 - - - -
79L TYR* 3.9 23.4 + - - +
109L GLU* 4.9 8.3 + - - +
111L GLU* 5.2 3.0 + - - -
7002L MRD 5.4 1.4 - - - +
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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