Contacts of the strand formed by residues 39 - 44 (chain A) in PDB entry 1H3F
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 THR 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 5.6 0.3 + - - -
37A PRO 4.7 2.8 + - - -
38A LEU* 1.3 71.4 - - - +
40A VAL* 1.3 58.8 + - - +
41A LYS 3.8 0.2 + - - -
71A LYS* 3.4 10.4 - - - +
73A VAL* 3.6 30.1 - - + -
186A ILE* 3.8 30.6 + - + +
187A ARG 3.9 10.5 + - - -
188A ALA* 3.9 2.6 - - - -
189A ASP* 2.8 39.1 + - - -
190A VAL 3.1 8.8 + - - +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.9 13.5 - - + +
39A THR* 1.3 74.4 - - - +
41A LYS* 1.3 61.8 + - - +
62A MET* 4.5 9.1 - - + +
65A PHE* 3.9 41.5 - - + -
70A HIS* 4.4 3.1 - - + -
71A LYS 2.7 14.5 + - - +
72A VAL* 3.3 11.9 - - + +
73A VAL 2.8 27.2 + - - +
190A VAL* 3.5 16.6 - - + +
192A MET* 3.6 34.5 - - + -
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR 3.8 0.4 + - - -
40A VAL* 1.3 73.3 - - - +
42A LEU* 1.3 67.3 + - - +
73A VAL 3.7 4.5 - - - +
75A ILE* 3.8 17.5 - - + -
179A GLN* 2.7 30.1 + - - +
180A ALA* 4.8 0.2 - - - +
182A ASP* 3.8 4.0 - - - -
183A SER* 2.7 33.0 + - - +
186A ILE* 3.7 20.6 - - + -
188A ALA* 3.8 6.1 - - + -
190A VAL 2.8 17.1 + - - +
191A GLU* 3.2 32.7 + - + +
192A MET* 2.8 32.2 + - - +
1433A TYE 3.4 22.2 + - - -
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL 4.1 0.2 + - - -
41A LYS* 1.3 80.0 - - - +
43A GLY* 1.3 71.8 + - - +
58A VAL* 4.0 20.9 - - + -
59A LEU* 3.7 21.1 - - + -
62A MET* 3.4 37.5 - - + -
73A VAL 3.2 6.0 + - - +
74A LEU* 3.5 13.6 - - + +
75A ILE* 2.9 24.3 + - - -
108A TYR* 3.9 15.3 - - - +
191A GLU* 5.5 0.4 - - - -
192A MET* 4.0 17.7 - - + +
193A GLY* 5.0 2.0 - - - +
1433A TYE 6.0 0.2 - - + -
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Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 4.4 0.6 - - - +
42A LEU* 1.3 87.4 - - - +
44A ALA* 1.3 60.1 + - - +
75A ILE* 3.3 10.5 - - - -
191A GLU* 5.1 0.4 + - - -
192A MET 5.4 0.4 + - - -
1433A TYE 3.3 55.1 - - - +
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 4.1 1.1 + - + -
43A GLY* 1.3 75.0 - - - +
45A ASP* 1.3 59.7 + - - +
46A PRO* 3.4 1.4 - - - +
74A LEU* 4.6 3.6 - - + -
75A ILE 3.0 10.2 + - - +
76A ILE* 3.7 6.4 - - + +
77A GLY* 2.8 31.6 + - - -
108A TYR* 3.4 49.1 - - + +
1433A TYE 4.2 4.4 - - - -
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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