Contacts of the strand formed by residues 32 - 38 (chain B) in PDB entry 4NLH
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 LEU 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B TYR* 3.6 45.8 - - + -
27B LEU 5.8 0.2 - - - +
30B ALA 3.5 1.0 + - - +
31B HIS* 1.3 75.6 - - - +
33B GLU* 1.3 63.6 + - - +
34B CYS 3.8 8.5 - - - +
52B ILE* 4.6 0.2 - - + -
85B LEU 3.3 0.3 - - - +
86B ALA* 3.3 4.0 - - - -
87B PHE* 2.8 54.7 + - + +
92B LEU* 4.0 16.4 - - + -
102B PHE* 3.4 31.4 - - + -
120B PHE* 3.8 24.5 - - + -
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Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TYR* 5.0 10.9 + - - -
31B HIS* 2.7 38.0 + - + +
32B LEU* 1.3 75.4 - - - +
34B CYS* 1.3 60.1 + - - +
35B HIS* 3.3 33.6 + - - +
84B VAL* 4.4 11.5 - - + +
85B LEU 3.6 3.8 - - - -
86B ALA* 4.9 5.2 - - + -
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Residues in contact with CYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 4.0 20.9 - - - -
32B LEU* 3.8 16.6 + - + -
33B GLU* 1.3 71.3 - - - +
35B HIS* 1.3 61.5 + - - +
36B TYR* 3.9 12.7 - - - -
50B VAL* 4.2 8.5 - - - -
83B CYS 3.7 0.5 - - - +
84B VAL* 3.4 3.7 - - - -
85B LEU* 2.9 42.9 + - + +
87B PHE* 3.9 9.2 - - + -
102B PHE* 3.8 36.3 - - + -
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Residues in contact with HIS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.6 7.4 - - - +
20B GLN* 2.9 48.6 + - + +
21B ASN* 5.3 12.6 - - + +
22B VAL* 5.1 1.2 - - - +
33B GLU* 3.3 34.5 + - + +
34B CYS* 1.3 73.6 - - - +
36B TYR* 1.3 63.1 + - - +
83B CYS 3.3 6.0 + - - +
84B VAL* 3.9 31.1 - - + +
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.1 16.6 - - + -
18B ILE 3.1 14.1 - - - +
19B PHE* 3.6 20.2 - + + -
20B GLN* 4.2 2.5 - - - -
34B CYS* 3.9 21.1 - - - -
35B HIS* 1.3 79.2 - - - +
37B THR* 1.3 63.9 + - - +
38B LEU* 4.2 6.7 - - + -
50B VAL* 3.9 15.5 - - + -
69B SER* 2.7 32.2 + - - -
70B PRO* 4.7 2.1 - - - +
81B VAL 4.0 0.2 - - - +
82B ASN* 3.5 4.6 - - - +
83B CYS* 2.9 63.4 + - + +
85B LEU* 3.6 25.3 - - + +
104B TYR* 4.0 12.3 - + - -
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.4 6.7 - - - +
18B ILE* 2.7 34.9 + - + -
20B GLN* 2.8 28.5 + - - +
36B TYR* 1.3 74.5 - - - +
38B LEU* 1.3 68.6 + - - +
39B THR* 3.3 12.8 + - + +
80B THR* 3.7 25.6 - - + -
81B VAL 3.3 8.1 - - - +
82B ASN* 2.5 24.5 + - - +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.1 11.2 - - + -
36B TYR* 4.2 8.7 - - + -
37B THR* 1.3 71.8 - - - +
39B THR* 1.3 63.8 + - - +
42B ILE* 3.7 16.6 - - + +
44B PRO* 4.2 16.6 - - + -
69B SER* 5.3 2.7 - - - +
70B PRO 5.9 0.4 - - - +
72B PRO* 3.6 31.4 - - + -
75B TYR* 5.5 2.9 - - + +
79B SER 3.6 2.4 - - - +
80B THR* 3.6 5.0 - - - -
81B VAL* 2.8 39.4 + - + +
83B CYS* 3.7 22.9 - - - -
104B TYR* 3.8 36.6 - - + +
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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