Contacts of the helix formed by residues 83 - 98 (chain D) in PDB entry 5SV1
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 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D GLN* 4.2 20.4 - - + +
54D ARG* 5.9 0.6 - - - +
55D LEU* 4.4 15.5 - - + -
58D GLU* 4.2 4.9 + - - +
81D LYS 4.5 7.0 - - - +
82D SER* 1.3 74.8 + - - +
84D SER* 1.3 61.0 + - - +
85D LEU 3.2 0.2 - - - -
86D HIS* 2.8 25.7 + - + +
87D LEU* 3.0 17.9 + - + +
122D VAL* 4.5 23.6 - - + -
205D PHE* 3.7 32.1 - - + -
209D LEU* 4.4 22.2 - - + -
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Residues in contact with SER 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D LEU* 3.9 5.9 - - - +
58D GLU* 3.1 24.1 + - - +
62D LEU* 4.2 15.9 - - - +
78D PHE* 4.4 7.2 - - - -
82D SER* 3.3 2.2 + - - -
83D LEU* 1.3 77.4 - - - +
85D LEU* 1.3 58.5 + - - +
87D LEU* 3.8 2.7 - - - +
88D LEU* 2.9 36.0 + - - +
209D LEU* 5.8 0.2 - - - +
212D VAL* 3.3 39.2 - - - +
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D ASN* 5.0 5.6 - - - +
75D ALA* 3.0 39.2 - - + +
76D ALA* 4.0 16.4 - - - +
78D PHE* 4.8 0.4 - - + -
79D GLY 3.8 18.6 - - - +
80D SER* 4.8 8.1 - - - +
82D SER* 3.5 21.0 + - - +
83D LEU 3.2 0.8 - - - -
84D SER* 1.3 78.6 - - - +
86D HIS* 1.3 60.1 + - - +
88D LEU* 4.5 5.6 - - + -
89D ASN* 2.9 60.6 + - - +
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Residues in contact with HIS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D SER 3.0 28.4 + - - -
81D LYS* 4.1 7.9 - - - -
82D SER 2.4 24.8 + - - -
83D LEU* 2.8 17.3 + - + +
85D LEU* 1.3 77.6 - - + +
87D LEU* 1.3 62.4 + - + +
89D ASN* 3.8 5.5 - - - +
90D GLU* 3.0 34.2 + - + +
118D ARG* 5.1 20.0 - - + +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D LEU 3.0 13.6 + - - +
84D SER* 3.9 5.2 - - - +
86D HIS* 1.3 74.5 - - + +
88D LEU* 1.3 61.7 + - - +
90D GLU* 2.8 19.9 + - - +
91D ALA* 2.9 12.0 + - - +
115D LEU* 3.8 23.2 - - + +
118D ARG* 3.6 34.1 - - + -
119D VAL* 4.9 3.6 - - + +
209D LEU* 4.0 20.4 - - + -
212D VAL* 3.9 12.1 - - + -
213D ALA* 3.7 38.8 - - + +
216D VAL* 4.6 12.1 - - + -
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LEU* 3.8 24.9 - - + -
68D LEU* 3.7 28.0 - - + -
71D ALA* 3.6 35.0 - - + +
72D ASN* 3.7 16.9 + - - +
75D ALA* 3.8 11.4 - - + -
84D SER* 2.9 19.3 + - - +
85D LEU* 4.3 5.8 - - + +
87D LEU* 1.3 76.4 - - - +
89D ASN* 1.3 58.9 + - - +
91D ALA* 3.3 3.6 + - - +
92D GLN* 2.9 30.1 + - - +
216D VAL* 3.4 26.7 - - + -
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Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D ASN* 4.0 10.6 + - - -
85D LEU* 2.9 55.2 + - - +
86D HIS* 3.9 6.5 + - - +
88D LEU* 1.3 77.4 - - - +
90D GLU* 1.3 59.1 + - + +
92D GLN* 4.1 4.5 - - - +
93D ASN* 2.9 28.8 + - - +
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Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D HIS* 3.0 16.9 + - + +
87D LEU* 2.8 10.6 + - - +
89D ASN* 1.3 76.8 - - + +
91D ALA* 1.3 64.8 + - - +
93D ASN* 3.3 1.1 + - - -
94D GLU* 2.9 20.3 + - - +
111D THR* 5.5 0.9 - - - -
114D ARG* 3.0 74.0 + - + +
115D LEU* 4.2 10.6 - - + +
118D ARG* 3.2 39.7 + - + +
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Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 4.6 11.4 - - + -
87D LEU 2.9 6.6 + - - +
88D LEU* 3.8 5.6 - - - +
90D GLU* 1.3 75.7 - - - +
92D GLN* 1.3 63.2 + - - +
94D GLU* 2.9 5.9 + - - +
95D LEU* 2.9 26.5 + - - +
111D THR* 4.0 25.0 - - + +
115D LEU* 4.9 1.0 - - + +
216D VAL* 3.7 30.3 - - + -
220D GLN* 4.2 7.5 + - - +
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Residues in contact with GLN 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 4.6 4.4 - - - +
69D ASN* 4.4 14.2 + - - +
72D ASN* 3.2 29.8 + - - +
88D LEU 2.9 17.0 + - - +
89D ASN* 4.1 6.3 - - - +
91D ALA* 1.3 75.8 - - - +
93D ASN* 1.3 58.4 + - - +
95D LEU* 3.0 23.3 + - - +
96D GLU* 2.9 51.6 + - - +
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Residues in contact with ASN 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ASN 2.9 20.8 + - - +
90D GLU* 3.8 5.2 - - - +
91D ALA 3.2 0.2 - - - -
92D GLN* 1.3 75.9 - - - +
94D GLU* 1.3 56.9 + - - +
96D GLU* 3.8 15.2 + - - +
97D LEU* 3.0 56.7 + - - +
114D ARG* 3.1 27.3 + - - +
66E ARG* 4.8 8.1 - - - +
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Residues in contact with GLU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLU 2.9 14.6 + - - +
91D ALA* 3.5 8.1 - - - +
93D ASN* 1.3 78.1 - - - +
95D LEU* 1.3 62.5 + - - +
97D LEU* 4.7 0.4 - - - -
98D SER* 3.1 31.8 + - - +
107D ILE* 4.4 5.6 - - + +
110D ARG* 3.2 39.5 + - + +
111D THR* 3.5 26.7 - - - +
114D ARG* 3.2 25.3 + - - +
218E LEU* 5.2 0.2 - - - +
222E ARG* 2.6 41.8 + - - -
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 3.8 29.2 - - + -
91D ALA 2.9 13.0 + - - +
92D GLN* 3.0 25.5 + - - +
94D GLU* 1.3 78.5 - - - +
96D GLU* 1.3 61.3 + - + +
98D SER* 3.7 3.3 + - - -
99D GLU* 3.6 20.4 + - - +
107D ILE* 3.9 31.6 - - + +
220D GLN* 3.7 11.9 - - + +
224D LEU* 4.3 17.9 - - + -
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Residues in contact with GLU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D GLN* 2.9 44.4 + - - +
93D ASN* 3.9 14.4 + - - +
95D LEU* 1.3 76.7 - - - +
97D LEU* 1.3 68.6 + - + +
99D GLU* 3.3 37.4 + - - +
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ASN* 3.0 43.9 + - - +
94D GLU 4.3 1.1 - - - +
96D GLU* 1.3 79.7 - - + +
98D SER* 1.3 58.4 + - - +
99D GLU 3.3 2.3 + - - +
114D ARG* 4.8 1.8 - - - +
66E ARG* 4.3 37.7 - - + +
222E ARG* 3.9 45.5 + - - +
226E LEU* 4.1 16.5 - - - +
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Residues in contact with SER 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLU* 3.1 24.1 + - - -
95D LEU 3.7 3.8 + - - -
96D GLU 3.2 1.2 - - - -
97D LEU* 1.3 74.0 - - - +
99D GLU* 1.3 67.1 + - - +
101D SER* 3.0 26.9 + - - +
107D ILE* 3.6 25.5 - - - +
110D ARG* 3.1 25.9 + - - -
222E ARG* 3.6 10.0 - - - +
226E LEU* 4.4 5.2 - - - -
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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