Contacts of the helix formed by residues 91 - 103 (chain D) in PDB entry 6YOV
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 91 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C GLY* 4.7 7.9 - - - -
48C ALA* 3.9 9.0 - - - -
89D THR* 3.9 19.3 - - + +
90D ILE* 1.3 79.6 - - - +
92D SER* 1.3 67.9 + - - +
93D ARG* 3.2 13.2 + - - +
94D GLU* 2.6 37.1 + - - +
95D ILE* 3.4 14.7 + - - +
40I G 6.5 0.4 - - - -
113J G 5.5 2.9 - - - +
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Residues in contact with SER 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLY* 3.6 28.2 - - - -
48C ALA* 4.0 7.5 - - - +
51C TYR* 3.7 14.9 - - - -
91D THR* 1.3 78.0 + - - +
93D ARG* 1.3 59.7 + - - +
95D ILE* 3.5 1.6 + - - +
96D GLN* 3.0 27.0 + - - +
119D VAL* 3.9 26.0 - - - +
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Residues in contact with ARG 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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75B GLU* 3.6 13.5 + - - +
76B HIS* 3.3 42.9 + - + +
78B LYS* 3.3 40.7 - - - +
91D THR* 3.0 11.9 + - - +
92D SER* 1.3 81.6 + - - +
94D GLU* 1.3 69.5 + - - +
96D GLN* 3.2 16.7 + - - +
97D THR* 3.1 23.8 + - - +
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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
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76B HIS* 3.8 28.7 + - + +
78D ALA* 4.1 14.4 - - + +
81D LEU* 3.3 18.7 - - + +
82D ALA* 4.7 6.6 - - - +
87D ARG* 5.0 10.7 + - - +
89D THR 4.3 7.5 - - - +
90D ILE* 4.1 18.2 - - + -
91D THR* 2.6 41.9 + - - +
93D ARG* 1.3 73.8 - - - +
95D ILE* 1.3 62.1 + - - +
97D THR 3.3 0.3 + - - -
98D ALA* 2.9 31.3 + - - +
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Residues in contact with ILE 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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35C LEU* 4.7 10.1 - - + -
48C ALA* 3.8 22.7 - - - +
51C TYR* 3.3 26.7 - - + -
52C LEU* 4.1 24.9 - - + +
74D ILE* 3.9 22.7 - - + +
78D ALA* 4.0 19.3 - - + -
90D ILE* 4.1 9.4 - - + -
91D THR 3.4 13.4 + - - +
92D SER 3.7 6.5 - - - +
93D ARG 3.2 0.2 - - - -
94D GLU* 1.3 76.9 - - - +
96D GLN* 1.3 62.7 + - - +
98D ALA* 3.1 5.9 + - - +
99D VAL* 2.9 31.5 + - + +
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Residues in contact with GLN 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C TYR* 3.0 30.5 + - + +
92D SER 3.0 11.7 + - - +
93D ARG* 3.2 21.4 + - - +
95D ILE* 1.3 78.6 - - - +
97D THR* 1.3 63.7 + - - +
99D VAL* 3.3 10.8 + - - +
100D ARG* 3.3 24.0 + - - +
112D VAL* 3.7 16.6 - - + +
116D THR* 2.9 31.1 + - - +
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Residues in contact with THR 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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72B THR* 4.0 17.3 - - + +
73B TYR* 5.4 0.4 - - + -
76B HIS* 2.8 45.3 + - + +
81D LEU* 3.6 22.9 - - + -
93D ARG* 3.1 6.9 + - - +
94D GLU 3.8 0.9 - - - -
96D GLN* 1.3 81.1 + - - +
98D ALA* 1.3 63.6 + - - +
100D ARG* 3.1 11.2 + - - +
101D LEU* 3.0 32.7 + - + +
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Residues in contact with ALA 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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74D ILE* 3.7 32.3 - - + +
77D GLU* 3.8 19.5 - - + -
78D ALA 4.0 4.3 - - - +
81D LEU* 3.9 1.3 - - + +
94D GLU 2.9 18.0 + - - +
95D ILE* 3.4 4.7 - - - +
97D THR* 1.3 76.6 - - - +
99D VAL* 1.3 63.6 + - - +
101D LEU* 3.2 7.2 + - - +
102D LEU* 3.0 30.3 + - - +
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Residues in contact with VAL 99 (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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51C TYR* 4.3 4.3 - - + -
55C VAL* 3.9 29.2 - - + -
74D ILE* 4.2 12.3 - - + -
95D ILE* 2.9 23.7 + - + +
96D GLN 3.5 8.7 - - - +
97D THR 3.2 0.2 - - - -
98D ALA* 1.3 77.0 - - - +
100D ARG* 1.3 56.5 + - - +
102D LEU* 3.2 0.8 + - - -
103D LEU* 2.8 46.5 + - + +
108D ALA* 3.8 13.5 - - - +
111D ALA* 3.7 27.1 - - + -
112D VAL* 4.0 6.7 - - + +
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Residues in contact with ARG 100 (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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69B ASP* 5.5 0.7 - - - +
72B THR* 4.7 18.2 - - + +
96D GLN* 3.3 20.6 + - - +
97D THR* 3.1 11.4 + - - +
99D VAL* 1.3 78.2 - - - +
101D LEU* 1.3 62.8 + - - +
103D LEU 3.2 15.7 - - - +
108D ALA* 4.5 10.1 - - + +
109D LYS* 5.5 9.5 - - - +
112D VAL* 3.9 37.0 - - + +
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Residues in contact with LEU 101 (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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69B ASP* 4.0 25.9 - - + +
72B THR* 3.8 25.4 - - + -
73B TYR* 3.6 46.4 - - + +
93B ARG* 2.8 30.3 + - - +
77D GLU* 4.3 9.4 - - + +
81D LEU* 4.4 6.3 - - + -
97D THR* 3.0 32.1 + - + +
98D ALA* 3.2 10.3 + - - +
100D ARG* 1.3 77.3 - - - +
102D LEU* 1.3 61.3 + - + +
103D LEU 4.9 0.2 - - - +
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Residues in contact with LEU 102 (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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93B ARG* 3.8 14.8 - - - +
97C LEU* 4.0 12.4 - - + +
73D ARG* 3.5 51.5 + - + +
74D ILE* 3.5 26.0 - - + +
77D GLU* 3.8 19.7 - - + +
98D ALA 3.0 19.3 + - - +
101D LEU* 1.3 79.5 - - - +
103D LEU* 1.3 72.6 + - + +
104D PRO* 3.9 4.7 - - - +
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Residues in contact with LEU 103 (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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55C VAL* 5.0 0.7 - - + -
59C LEU* 3.9 33.9 - - + -
97C LEU* 4.2 20.2 - - + -
70D ILE* 5.4 2.2 - - + -
74D ILE* 4.9 11.2 - - + -
99D VAL* 2.8 28.4 + - + +
100D ARG 3.2 17.3 - - - +
101D LEU 4.7 0.2 - - - -
102D LEU* 1.3 86.4 - - + +
104D PRO* 1.3 64.7 - - + +
105D GLY 4.1 0.3 + - - -
107D LEU* 3.9 11.7 - - + +
108D ALA* 3.3 34.6 - - + +
111D ALA* 4.0 12.1 - - + -
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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