Contacts of the strand formed by residues 39 - 44 (chain H) in PDB entry 5FLM
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 39 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H PHE* 3.4 37.7 - - + -
28H LEU 4.3 0.2 - - - -
29H HIS* 3.6 1.0 - - - -
30H CYS* 2.9 41.8 + - + +
37H MET 3.5 0.8 + - - +
38H ASP* 1.3 82.9 + - - +
40H ILE* 1.3 71.9 + - - +
41H LEU* 4.2 16.6 - - + -
56H PHE* 4.2 13.0 - - + -
58H LEU* 3.6 13.2 - - + -
123H MET* 3.7 26.7 - - + -
124H ARG 3.3 15.9 - - - +
125H LEU* 3.9 17.3 - - + -
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Residues in contact with ILE 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A TYR* 3.4 33.0 - - + +
621A ILE* 4.2 13.2 - - + -
27H ARG* 3.6 30.5 - - + +
28H LEU 3.5 3.4 - - - -
29H HIS* 3.4 17.3 - - + +
38H ASP* 4.6 12.6 - - - +
39H LEU* 1.3 78.3 - - - +
41H LEU* 1.3 62.4 + - - +
42H ASP* 5.2 0.4 - - - +
122H LEU 4.1 1.5 - - - +
123H MET* 3.1 6.1 - - - +
124H ARG* 2.8 60.6 + - + +
126H GLN* 6.1 1.6 - - - +
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Residues in contact with LEU 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H ARG* 3.4 1.5 - - - -
28H LEU* 2.8 43.4 + - + +
39H LEU* 4.2 24.7 - - + -
40H ILE* 1.3 75.8 - - - +
42H ASP* 1.3 76.6 + - - +
43H VAL* 3.6 25.0 + - + +
56H PHE* 5.3 1.3 - - + -
58H LEU* 5.1 2.2 - - + -
92H MET* 4.2 2.0 - - + -
118H TYR* 4.1 6.3 - - + -
122H LEU 3.9 1.3 - - - +
123H MET* 3.7 25.8 - - + -
143H LEU* 3.7 32.8 - - + -
145H MET* 3.7 18.4 - - + -
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Residues in contact with ASP 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ARG* 2.5 37.0 + - - -
25H VAL* 4.1 15.0 - - + -
26H SER 3.7 2.7 - - - -
27H ARG* 2.8 38.4 + - - +
40H ILE* 5.2 0.6 - - - +
41H LEU* 1.3 73.3 + - - +
43H VAL* 1.3 59.6 + - - +
92H MET* 4.0 10.4 - - - +
118H TYR* 5.6 0.2 - - - -
121H LEU* 3.5 24.1 - - + +
122H LEU* 2.9 37.1 + - - +
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Residues in contact with VAL 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H VAL* 3.3 5.5 - - - -
26H SER* 2.9 40.4 + - - +
28H LEU* 3.7 23.8 - - + -
41H LEU* 3.6 32.3 - - + +
42H ASP* 1.3 77.5 - - - +
44H ASN* 1.3 77.6 + - - +
45H ILE* 3.6 0.8 + - + -
48H TYR* 4.1 20.0 - - + +
50H VAL* 4.6 7.2 - - + -
90H TYR* 3.9 22.4 - - + +
121H LEU* 5.1 0.2 - - - -
145H MET* 4.8 1.8 - - - -
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Residues in contact with ASN 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A PHE* 3.3 37.9 - - + -
579A ILE* 3.7 19.0 - - + +
585A LEU* 4.1 1.2 - - - +
24H ARG* 2.9 19.9 - - - +
25H VAL* 4.4 2.8 - - - +
42H ASP 4.4 0.2 + - - -
43H VAL* 1.3 80.6 - - - +
45H ILE* 1.3 78.0 + - - +
46H GLN* 3.4 12.6 + - - +
47H ILE* 3.5 31.5 + - + +
48H TYR* 3.3 21.8 + - - +
90H TYR* 3.5 9.7 + - + +
121H LEU* 4.8 2.7 - - + +
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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