Contacts of the helix formed by residues 90 - 102 (chain N) in PDB entry 5GSE
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 90 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215I G 5.5 4.7 - - - +
40J G 5.9 0.2 - - - -
41J A 5.6 1.7 + - - -
44M GLY* 4.8 10.0 + - - +
46M GLY 6.2 0.9 - - - +
47M ALA* 4.0 5.4 - - - -
86N ARG* 4.9 3.8 - - - -
88N THR* 3.7 16.8 + - - -
89N ILE* 1.3 74.0 - - - +
91N SER* 1.3 79.2 + - - +
92N ARG* 3.1 11.4 - - + +
93N GLU* 3.0 21.4 + - - +
94N ILE* 3.3 25.3 + - - +
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Residues in contact with SER 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M GLY* 3.9 27.3 - - - -
47M ALA* 4.2 10.9 - - - +
50M TYR* 4.0 19.7 - - - -
90N THR* 1.3 82.1 - - - +
92N ARG* 1.3 57.4 + - - +
94N ILE* 3.5 6.3 + - - +
95N GLN* 2.9 28.6 + - - +
118N VAL* 4.9 7.6 - - - +
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Residues in contact with ARG 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J A 5.6 5.4 - - - -
74L GLU 2.6 30.3 + - - -
75L HIS* 3.0 39.1 + - + +
77L LYS* 3.2 31.6 - - - +
86N ARG* 5.9 2.9 - - - +
90N THR* 3.1 8.1 - - + +
91N SER* 1.3 77.3 + - - +
93N GLU* 1.3 60.5 + - - +
95N GLN* 3.2 23.2 + - - +
96N THR* 2.7 39.9 + - + +
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Residues in contact with GLU 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L HIS* 2.9 28.0 + - - +
77N ALA* 3.9 29.3 - - + +
80N LEU* 3.7 5.1 - - + +
81N ALA* 4.1 17.2 - - + +
84N ASN* 5.4 0.5 + - - +
86N ARG* 3.7 20.6 + - - -
88N THR 3.6 9.8 - - - +
89N ILE* 4.6 2.9 - - + -
90N THR* 3.0 41.8 + - - +
92N ARG* 1.3 80.4 - - - +
94N ILE* 1.3 58.0 + - - +
96N THR* 3.3 6.0 + - - -
97N ALA* 2.9 32.1 + - - +
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Residues in contact with ILE 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M LEU* 5.3 2.5 - - + -
47M ALA* 3.8 20.6 - - + +
50M TYR* 3.4 36.1 - - + -
51M LEU* 4.2 27.4 - - + +
73N ILE* 4.3 8.9 - - + +
74N ALA* 6.1 0.9 - - - -
77N ALA* 4.1 8.3 - - + -
89N ILE* 3.3 25.6 - - + -
90N THR 3.3 16.2 + - - +
91N SER* 3.8 8.5 - - - +
92N ARG 3.3 0.2 - - - -
93N GLU* 1.3 78.4 - - - +
95N GLN* 1.3 58.2 + - - +
97N ALA* 3.8 5.8 - - - +
98N VAL* 2.9 34.7 + - + +
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Residues in contact with GLN 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M TYR* 3.3 35.5 + - + +
91N SER 2.9 17.4 + - - +
92N ARG* 3.2 26.1 + - - +
93N GLU 3.2 0.2 - - - -
94N ILE* 1.3 75.0 - - - +
96N THR* 1.3 65.1 + - + +
98N VAL* 3.3 6.3 + - - +
99N ARG* 2.9 49.2 + - - +
111N VAL* 3.6 14.4 - - + +
115N THR* 5.0 4.5 - - - -
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Residues in contact with THR 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L THR* 4.4 5.1 + - - +
74L GLU 5.4 0.4 - - - -
75L HIS* 2.8 47.2 + - + +
80N LEU* 3.2 19.9 - - - +
92N ARG* 2.7 23.4 + - + +
93N GLU 3.3 0.3 + - - -
95N GLN* 1.3 75.0 - - + +
97N ALA* 1.3 58.3 + - - +
99N ARG* 3.3 38.3 + - - +
100N LEU* 3.0 31.5 + - - +
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Residues in contact with ALA 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N ILE* 3.8 13.0 - - + +
76N GLU* 3.7 35.0 - - + -
77N ALA* 3.8 11.0 - - + +
80N LEU* 3.8 2.8 - - + +
93N GLU 2.9 19.6 + - - +
94N ILE 3.8 4.7 - - - +
96N THR* 1.3 78.1 + - - +
98N VAL* 1.3 56.6 + - - +
100N LEU* 3.0 4.0 + - - +
101N LEU* 2.9 33.7 + - - +
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Residues in contact with VAL 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M TYR* 5.3 1.1 - - + -
54M VAL* 4.2 17.9 - - + -
73N ILE* 3.6 33.0 - - + -
94N ILE* 2.9 24.3 + - + +
95N GLN* 3.6 8.3 - - - +
97N ALA* 1.3 75.5 - - - +
99N ARG* 1.3 62.6 + - - +
101N LEU* 4.6 2.7 - - - +
102N LEU* 3.1 34.2 + - + +
107N ALA* 4.1 11.1 - - - +
110N ALA* 3.9 27.1 - - + -
111N VAL* 4.6 8.3 - - + +
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Residues in contact with ARG 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L ARG* 6.2 0.3 - - - -
68L ASP* 5.5 0.9 - - - +
71L THR* 3.7 31.2 - - + +
74L GLU* 3.3 31.1 + - - +
95N GLN* 2.9 38.4 + - - +
96N THR* 3.4 34.6 - - - +
97N ALA 3.2 0.4 - - - -
98N VAL* 1.3 77.4 - - + +
100N LEU* 1.3 62.4 + - + +
102N LEU 3.7 10.0 - - - +
107N ALA* 4.4 14.5 - - + +
108N LYS* 6.0 3.8 - - - +
111N VAL* 4.8 18.4 - - + -
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Residues in contact with LEU 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L ASP* 3.8 34.2 - - + +
71L THR* 3.2 28.7 - - + +
72L TYR* 3.4 24.5 - - + +
92L ARG* 3.4 26.0 + - - +
76N GLU* 3.4 36.8 - - + +
80N LEU* 4.6 5.8 - - + -
96N THR* 3.0 19.0 + - - +
97N ALA* 3.0 9.5 + - - +
99N ARG* 1.3 81.3 - - - +
101N LEU* 1.3 62.0 + - - +
102N LEU 4.4 1.4 - - - +
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Residues in contact with LEU 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L ARG* 3.2 31.3 + - - +
96M LEU* 4.2 10.2 - - + +
72N ARG* 3.4 59.8 + - + +
73N ILE* 3.5 20.2 - - + +
76N GLU* 4.3 11.7 - - + +
79N ARG* 5.9 1.6 - - - +
97N ALA 2.9 18.6 + - - +
98N VAL* 5.1 0.2 - - - -
100N LEU* 1.3 76.2 - - + +
102N LEU* 1.3 75.9 + - + +
103N PRO* 3.6 5.2 - - - +
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Residues in contact with LEU 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M VAL* 6.0 0.7 - - + -
58M LEU* 3.7 37.2 - - + -
96M LEU* 4.0 17.7 - - + -
69N ILE* 5.4 2.5 - - + -
73N ILE* 5.0 15.0 - - + -
98N VAL* 3.1 20.5 + - + +
99N ARG 3.7 14.4 - - - +
100N LEU 4.4 1.8 - - - +
101N LEU* 1.3 88.4 - - + +
103N PRO* 1.3 70.6 - - + +
104N GLY 3.8 1.0 + - - -
106N LEU* 3.9 12.6 - - + -
107N ALA* 3.7 15.7 - - + +
110N ALA* 3.6 31.2 - - + -
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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