Contacts of the strand formed by residues 126 - 134 (chain F) in PDB entry 5MG3
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 ALA 126 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240D GLN 3.5 5.2 + - - +
241D LEU* 3.8 12.8 - - - +
60F ILE* 4.6 1.6 - - + -
61F THR 3.2 11.4 - - - +
62F LEU* 4.1 3.6 - - + -
71F MET* 3.5 28.7 - - + -
118F ILE* 3.9 9.0 - - + -
119F ASN* 3.4 21.9 - - - +
120F GLU 6.1 0.4 - - - +
121F SER* 3.5 5.3 + - - +
124F GLN* 3.3 16.2 - - + +
125F ASN* 1.3 71.8 - - - +
127F ALA* 1.3 65.0 + - - +
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Residues in contact with ALA 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D LEU* 3.2 25.6 - - + +
263D ILE* 3.8 24.0 - - + -
60F ILE* 3.4 3.3 - - - -
61F THR* 2.9 37.6 + - - +
118F ILE* 3.7 5.2 - - - -
119F ASN* 3.6 18.4 - - - +
126F ALA* 1.3 75.5 - - - +
128F VAL* 1.3 64.1 + - - +
129F LYS* 4.2 0.5 - - - +
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Residues in contact with VAL 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ILE* 3.5 4.9 - - - +
264D GLN* 2.7 60.0 + - + +
381D ASN* 3.6 20.2 - - - +
58F ILE* 4.4 12.6 - - + -
59F GLU 3.7 10.5 - - - +
60F ILE* 4.2 9.0 - - + -
115F LEU 5.8 0.4 - - - +
118F ILE* 3.6 15.3 - - + +
119F ASN* 2.8 24.9 + - - +
127F ALA* 1.3 72.7 - - - +
129F LYS* 1.3 55.7 + - - +
130F ARG 4.1 13.9 - - - +
131F ILE* 5.6 2.5 - - + -
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Residues in contact with LYS 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D PRO* 2.8 34.0 + - - +
262D GLY 3.3 24.5 - - - +
263D ILE* 4.7 1.6 - - - -
264D GLN* 3.5 16.1 + - - +
444D THR* 4.9 0.5 - - - -
445D LEU* 3.6 45.9 + - + +
59F GLU* 2.9 17.0 + - + +
60F ILE 3.7 20.0 - - - +
61F THR* 3.1 16.6 + - - +
93F ASP* 2.9 39.6 + - + +
95F MET* 5.2 0.4 - - - -
127F ALA 4.2 0.4 - - - +
128F VAL* 1.3 76.2 - - - +
130F ARG* 1.4 63.6 + - - +
269F VAL* 4.1 4.2 - - - +
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Residues in contact with ARG 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D GLN* 4.0 10.5 - - - +
445D LEU* 3.8 23.6 - - + +
446D GLY* 3.5 26.9 - - - +
449D ASN* 3.7 11.1 + - - -
57F VAL 5.8 0.2 - - - +
58F ILE* 3.9 4.2 - - - +
59F GLU* 2.6 67.5 + - - +
128F VAL* 3.9 4.1 - - - +
129F LYS* 1.4 78.7 - - - +
131F ILE* 1.4 64.1 + - - +
132F GLU* 3.5 34.9 + - + +
269F VAL* 6.1 1.4 - - - +
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Residues in contact with ILE 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D GLN* 4.2 15.0 - - - +
56F THR* 5.5 4.7 - - + -
57F VAL 3.4 11.0 - - - +
58F ILE* 4.8 14.1 - - + -
80F PHE* 6.1 3.6 - - + -
107F GLY* 3.3 28.5 - - - +
108F GLN* 3.3 25.7 + - - +
115F LEU* 3.7 29.4 - - + -
128F VAL* 5.6 2.7 - - + -
130F ARG* 1.4 75.1 - - - +
132F GLU* 1.4 76.7 + - - +
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Residues in contact with GLU 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LEU* 3.7 32.2 - - + +
56F THR* 3.4 9.9 - - - +
57F VAL* 2.8 40.7 + - + +
59F GLU* 5.0 2.2 - - - +
108F GLN* 4.1 5.9 + - - +
130F ARG* 3.5 35.0 + - + +
131F ILE* 1.4 81.7 - - - +
133F PHE* 1.4 69.0 + - - +
134F VAL* 5.7 1.2 - - - +
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Residues in contact with PHE 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LEU* 3.8 0.6 - - - +
55F GLY 3.6 4.3 - - - -
56F THR* 4.0 14.8 - - - -
100F PRO* 4.2 5.2 - - + -
101F ALA* 3.5 37.2 - - + -
106F GLY* 4.0 8.3 - - - -
107F GLY* 3.3 35.4 - - - -
108F GLN* 4.4 14.7 + - + +
132F GLU* 1.4 82.9 + - - +
134F VAL* 1.4 81.9 + - - +
135F GLY* 4.4 13.5 - - - -
136F PRO* 5.8 0.9 - - + -
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Residues in contact with VAL 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LEU* 3.2 48.7 - - + +
51F ASP* 4.9 3.4 - - - +
54F GLY* 3.5 2.4 - - - -
55F GLY 3.0 26.2 + - - +
100F PRO* 3.9 3.5 - - - +
132F GLU* 5.7 1.6 - - - +
133F PHE* 1.4 86.2 - - - +
135F GLY* 1.4 63.5 + - - +
138F VAL* 4.4 8.7 - - + -
139F GLY* 3.6 28.9 - - - +
142F LEU* 4.4 8.7 - - + -
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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