Contacts of the strand formed by residues 104 - 108 (chain X) in PDB entry 1SGF
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 MET 104 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53X LEU* 3.3 9.6 - - - +
54X THR* 2.9 42.1 + - + +
55X ALA 3.5 26.7 - - - +
56X ALA* 3.9 2.7 - - - +
58X CYS* 4.2 1.8 - - + -
59X TYR* 3.8 19.3 - - - +
64X TYR* 3.3 31.6 - - + +
88X ALA* 5.2 0.4 - - - -
89X ILE 3.5 19.5 - - - +
90X PRO* 3.9 23.3 - - + -
103X LEU* 1.3 79.3 - - - +
105X LEU* 1.3 64.1 + - - +
106X LEU* 3.6 24.0 - - + -
237X TRP* 4.8 1.8 - - - -
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Residues in contact with LEU 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X LEU* 4.2 18.4 - - + -
51X TRP* 4.4 26.2 - - + -
52X VAL 3.6 11.7 - - - +
53X LEU* 3.8 22.2 - - + -
87X LYS 3.4 2.6 - - - +
89X ILE* 3.0 42.6 + - + +
104X MET* 1.3 75.0 - - - +
106X LEU* 1.3 63.0 + - - +
237X TRP* 3.8 22.0 - - + -
238X ILE* 4.3 17.7 - - + +
241X THR* 4.0 28.5 - - + -
242X MET* 5.0 3.8 - - + +
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Residues in contact with LEU 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X VAL* 4.2 17.5 - - + -
51X TRP* 3.7 6.9 - - - -
52X VAL* 2.8 44.0 + - + +
54X THR* 4.0 18.8 - - + -
64X TYR* 4.3 17.0 - - + -
66X VAL* 4.1 13.9 - - + -
85X VAL* 3.6 31.4 - - + -
87X LYS 3.3 2.5 - - - -
88X ALA* 4.5 4.9 - - - -
104X MET* 3.6 32.5 - - + -
105X LEU* 1.3 83.8 - - - +
107X ARG* 1.3 61.7 + - - +
108X LEU 4.1 0.5 + - - -
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Residues in contact with ARG 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X ASN* 3.6 32.0 + - - +
51X TRP* 3.6 37.2 - - + +
85X VAL* 3.2 5.4 - - - +
86X SER* 2.8 35.2 + - - +
87X LYS* 2.8 59.2 + - + +
106X LEU* 1.3 74.1 - - - +
108X LEU* 1.3 73.8 + - - +
109X SER* 5.5 2.4 + - - +
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Residues in contact with LEU 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X LEU* 4.7 3.8 - - + -
49X ARG 4.1 10.3 - - - +
50X ASN* 3.3 37.7 + - - +
51X TRP 4.7 0.2 - - - +
52X VAL* 4.0 21.8 - - + -
66X VAL* 3.8 32.3 - - + -
68X LEU* 4.7 3.4 - - + -
83X ARG* 4.4 14.1 - - + -
84X LEU 3.7 2.7 - - - -
85X VAL* 4.3 8.7 - - + -
86X SER* 4.2 1.1 + - - -
106X LEU 5.0 0.4 - - - +
107X ARG* 1.3 90.7 + - - +
109X SER* 1.3 63.0 + - - +
110X LYS 3.0 24.4 + - - +
112X ALA* 4.2 14.4 - - + -
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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