Contacts of the helix formed by residues 93 - 106 (chain F) in PDB entry 5GAG
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 GLY 93 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B A 5.4 1.5 + - - -
32F GLU 4.7 1.4 + - - -
92F ARG* 1.3 75.3 - - - +
94F GLU* 1.3 65.1 + - - -
96F MET* 3.1 15.7 + - - +
97F TRP* 3.0 33.2 + - - -
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Residues in contact with GLU 94 (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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2F ALA* 3.2 32.0 - - - +
5F HIS* 5.4 3.8 + - - +
92F ARG 3.4 1.2 + - - -
93F GLY* 1.3 70.9 - - - -
95F ARG* 1.3 63.2 + - + +
97F TRP* 3.0 15.6 + - - +
98F GLU* 2.9 48.3 + - - +
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Residues in contact with ARG 95 (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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61F SER 4.7 5.9 + - - +
62F GLY* 3.9 24.8 + - - -
63F GLN* 3.8 19.0 - - - +
91F LEU* 3.8 19.3 - - + +
92F ARG 3.5 6.4 + - - +
93F GLY 3.3 0.6 - - - -
94F GLU* 1.3 77.6 - - + +
96F MET* 1.3 60.8 + - - +
98F GLU* 3.7 29.3 + - - +
99F PHE* 3.0 31.9 + - - +
102F ARG* 4.6 4.0 + - - +
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Residues in contact with MET 96 (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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31F VAL* 3.5 29.6 - - + +
32F GLU 3.1 31.9 - - - +
33F LYS* 3.8 5.8 - - - -
34F ILE* 3.5 28.1 - - + +
91F LEU* 3.8 13.1 - - - +
92F ARG* 3.4 18.0 + - - -
93F GLY* 3.1 16.6 + - - +
95F ARG* 1.3 79.3 - - - +
97F TRP* 1.3 95.9 + - + +
99F PHE* 3.9 2.3 - - - +
100F PHE* 2.9 29.1 + - - +
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Residues in contact with TRP 97 (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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2F ALA* 3.8 17.6 + - - +
4F LEU* 4.2 11.0 - - + +
5F HIS* 3.2 63.2 + + + +
8F TYR* 4.6 7.6 - + + -
30F ARG* 6.1 1.3 - - + -
31F VAL* 3.9 36.6 - - + -
93F GLY* 3.0 30.2 + - - -
94F GLU* 3.0 13.9 + - - +
96F MET* 1.3 94.6 - - + +
98F GLU* 1.3 66.9 + - - +
100F PHE* 3.0 15.6 + + + +
101F GLU* 2.9 23.9 + - - +
173F PHE* 3.8 29.6 - + - -
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Residues in contact with GLU 98 (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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2F ALA* 3.7 24.5 - - + +
94F GLU* 2.9 40.2 + - - +
95F ARG* 3.7 31.4 + - - +
97F TRP* 1.3 73.4 - - - +
99F PHE* 1.3 59.7 + - - +
101F GLU* 3.1 7.9 + - - +
102F ARG* 2.9 42.3 + - + +
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Residues in contact with PHE 99 (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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34F ILE* 3.7 26.2 - - + -
36F LEU* 3.5 35.4 - - + -
60F ILE* 3.7 21.5 - - + -
61F SER* 4.7 0.2 - - - -
91F LEU* 4.1 13.5 - - + -
95F ARG 3.0 18.8 + - - +
96F MET 4.1 0.7 - - - +
98F GLU* 1.3 77.5 - - - +
100F PHE* 1.3 58.6 + - - +
102F ARG* 3.3 33.8 - - + +
103F LEU* 2.9 37.9 + - + +
138F PHE* 4.0 10.8 - + - -
154F ILE* 3.5 32.8 - - + -
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Residues in contact with PHE 100 (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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4F LEU* 3.9 15.5 - - + -
31F VAL* 5.1 6.7 - - + -
34F ILE* 4.0 17.5 - - + -
96F MET 2.9 20.8 + - - +
97F TRP* 3.0 26.2 + + + +
99F PHE* 1.3 83.4 - + - +
101F GLU* 1.3 57.1 + - - +
103F LEU* 3.6 8.1 - - + +
104F ILE* 3.0 56.9 + - + +
156F ILE* 4.6 14.1 - - + -
170F LEU* 4.1 23.1 - - + -
173F PHE* 3.8 32.3 - + + -
175F PHE* 4.0 17.3 - + - -
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Residues in contact with GLU 101 (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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2F ALA 4.1 12.1 + - - -
3F LYS* 3.4 42.4 + - - +
4F LEU* 3.5 25.9 - - + +
97F TRP 2.9 8.8 + - - +
98F GLU* 3.4 8.7 - - - +
100F PHE* 1.3 74.9 - - - +
102F ARG* 1.3 60.6 + - + +
104F ILE* 4.5 1.6 - - - +
105F THR* 2.9 50.6 + - - +
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Residues in contact with ARG 102 (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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60F ILE* 2.9 22.6 + - - +
61F SER 3.6 20.0 + - - -
62F GLY* 5.5 0.4 - - - -
95F ARG* 4.6 4.0 + - - +
98F GLU* 2.9 26.9 + - + +
99F PHE* 3.3 43.6 - - - +
101F GLU* 1.3 75.7 - - + +
103F LEU* 1.3 64.2 + - - +
106F ILE* 3.3 27.9 + - + +
107F ALA* 3.3 19.4 + - - +
138F PHE* 5.3 4.2 - - + -
139F PRO* 5.9 0.3 - - - +
140F GLU* 3.3 25.6 + - - +
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Residues in contact with LEU 103 (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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99F PHE* 2.9 27.2 + - + +
100F PHE* 3.6 12.3 - - + +
102F ARG* 1.3 79.1 - - - +
104F ILE* 1.3 65.6 + - + +
107F ALA* 3.6 7.1 + - + -
108F VAL* 2.9 46.4 + - + +
130F MET* 4.7 8.5 - - - -
132F VAL* 5.8 2.7 - - + -
137F ILE* 6.4 1.1 - - + -
138F PHE* 4.1 18.8 - - + -
154F ILE* 3.9 42.2 - - + -
156F ILE* 5.5 1.3 - - + -
175F PHE* 4.3 22.4 - - + -
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Residues in contact with ILE 104 (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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4F LEU* 4.6 7.6 - - + -
100F PHE* 3.0 54.8 + - + +
101F GLU* 4.1 3.6 - - - +
103F LEU* 1.3 79.0 - - + +
105F THR* 1.3 68.1 + - - +
108F VAL* 3.8 11.5 - - - +
109F PRO* 3.4 14.2 - - - +
173F PHE* 4.0 20.2 - - + +
174F ASP* 3.8 19.7 - - + +
175F PHE* 3.9 22.7 - - + -
176F PRO* 4.5 9.2 - - + +
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Residues in contact with THR 105 (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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101F GLU* 2.9 38.3 + - - +
104F ILE* 1.3 77.1 - - - +
106F ILE* 1.3 75.1 + - + +
109F PRO* 3.1 17.5 - - - +
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Residues in contact with ILE 106 (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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101F GLU 5.8 0.2 - - - -
102F ARG* 3.3 29.1 + - + +
104F ILE 3.5 0.4 - - - -
105F THR* 1.3 96.7 - - + +
107F ALA* 1.3 69.1 + - - +
109F PRO* 3.1 14.1 - - - +
110F ARG* 3.6 20.3 + - + +
137F ILE 4.8 0.2 - - - -
139F PRO* 3.8 26.7 - - + -
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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