Contacts of the helix formed by residues 87 - 99 (chain D) in PDB entry 6K1J
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 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C GLY* 4.9 1.3 - - - -
47C ALA* 3.9 6.1 - - - -
201C CL 3.7 17.9 - - + -
85D THR* 3.8 21.5 - - + +
86D ILE* 1.3 76.1 - - - +
88D SER* 1.3 59.4 + - - +
89D ARG* 3.0 22.8 + - - +
90D GLU* 2.7 37.4 + - - +
91D ILE* 3.2 12.6 + - - +
-33I G 5.6 2.2 - - - +
-32I A 6.1 1.6 - - - +
37J A 6.0 0.4 - - - +
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Residues in contact with SER 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLY* 3.7 27.1 - - - -
47C ALA* 3.8 8.5 - - - +
50C TYR* 3.8 20.7 - - - -
201C CL 3.5 11.6 - - - +
87D THR* 1.3 73.2 + - - +
89D ARG* 1.3 56.6 + - - +
91D ILE* 3.7 7.1 - - - +
92D GLN* 3.1 28.4 + - - +
115D VAL* 4.4 12.5 - - - +
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Residues in contact with ARG 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLU 3.1 26.1 + - - -
75B HIS* 2.7 41.4 + - + +
77B LYS* 3.6 38.6 - - - +
87D THR* 3.1 13.6 + - - +
88D SER* 1.3 78.2 + - - +
90D GLU* 1.3 65.8 + - - +
92D GLN* 3.6 5.1 + - - +
93D THR* 3.2 26.3 + - - +
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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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75B HIS* 2.7 36.7 + - + +
74D ALA* 4.2 23.1 - - + +
77D LEU* 4.1 4.5 - - + +
78D ALA* 4.3 14.3 - - + +
83D ARG* 5.1 10.6 - - - +
85D THR 3.2 13.9 - - - +
86D ILE* 4.2 15.3 - - + -
87D THR* 2.7 44.8 + - - +
89D ARG* 1.3 74.7 + - - +
91D ILE* 1.3 66.6 + - - +
92D GLN 2.9 2.5 + - - -
93D THR* 3.0 4.5 + - - -
94D ALA* 2.9 25.4 + - - +
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Residues in contact with ILE 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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34C LEU* 4.9 5.6 - - + -
47C ALA* 3.8 26.9 - - + +
50C TYR* 3.3 27.1 - - + -
51C LEU* 3.9 32.1 - - + +
70D ILE* 4.1 19.4 - - + +
71D ALA* 5.5 1.6 - - - -
74D ALA* 4.5 6.5 - - + -
86D ILE* 4.1 18.6 - - + -
87D THR 3.2 11.5 + - - +
88D SER* 3.7 7.6 - - - +
90D GLU* 1.3 75.8 - - - +
92D GLN* 1.3 56.7 + - - +
94D ALA* 3.5 7.5 + - - +
95D VAL* 3.1 29.9 + - + +
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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
----------------------------------------------------------
50C TYR* 2.4 49.9 + - + +
88D SER 3.1 17.3 + - - +
89D ARG* 4.0 7.2 - - - +
90D GLU 3.0 0.8 - - - -
91D ILE* 1.3 74.0 - - - +
93D THR* 1.3 67.9 + - - +
95D VAL* 2.8 14.4 + - - +
96D ARG* 2.9 42.3 + - - +
108D VAL* 3.5 21.3 - - + +
112D THR* 3.5 8.9 + - - +
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Residues in contact with THR 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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71B THR* 3.7 33.4 - - + +
75B HIS* 2.7 25.5 + - + +
77D LEU* 3.4 30.5 - - + -
89D ARG* 3.2 6.6 + - - +
90D GLU 3.0 2.5 + - - -
92D GLN* 1.3 76.6 - - - +
94D ALA* 1.3 58.2 + - - +
96D ARG* 2.9 26.2 + - - +
97D LEU* 3.0 19.8 + - + +
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Residues in contact with ALA 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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70D ILE* 4.0 15.9 - - + +
73D GLU* 3.7 26.9 - - + -
74D ALA* 4.0 12.8 - - - +
77D LEU* 4.4 1.9 - - + +
90D GLU 2.9 15.6 + - - +
91D ILE* 3.5 6.5 - - - +
93D THR* 1.3 76.3 - - - +
95D VAL* 1.3 57.8 + - - +
97D LEU* 3.5 8.1 + - - +
98D LEU* 3.1 35.4 + - - +
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 4.6 1.3 - - + -
54C VAL* 3.8 30.7 - - + -
70D ILE* 4.2 17.3 - - + -
91D ILE* 3.1 20.6 + - + +
92D GLN* 2.8 11.8 + - - +
94D ALA* 1.3 75.4 - - - +
96D ARG* 1.3 58.6 + - - +
97D LEU 3.3 0.2 - - - -
98D LEU* 4.8 1.6 - - - -
99D LEU* 3.0 51.5 + - + +
104D ALA* 4.3 3.4 - - - +
107D ALA* 4.1 10.8 - - + -
108D VAL* 3.9 24.0 - - + +
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Residues in contact with ARG 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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67B ARG* 5.7 4.3 - - - -
68B ASP* 5.0 2.3 - - - +
71B THR* 4.3 16.8 + - + +
92D GLN* 2.9 39.9 + - - +
93D THR* 2.9 12.3 + - - +
95D VAL* 1.3 75.7 - - - +
97D LEU* 1.3 62.4 + - - +
99D LEU 3.6 11.3 - - - +
104D ALA* 4.6 10.8 - - + +
105D LYS* 6.0 2.6 - - - +
108D VAL* 3.5 36.6 - - + +
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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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68B ASP* 3.7 37.6 - - + +
71B THR* 3.5 28.0 - - + +
72B TYR* 3.7 24.5 - - + +
92B ARG* 3.3 32.2 + - - +
73D GLU* 3.7 25.4 - - + +
77D LEU* 5.0 2.0 - - + -
93D THR* 3.0 26.8 + - + +
94D ALA* 3.6 12.1 - - - +
95D VAL 3.3 0.2 - - - -
96D ARG* 1.3 77.2 - - - +
98D LEU* 1.3 60.0 + - - +
99D LEU 4.7 1.2 - - - +
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Residues in contact with LEU 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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92B ARG* 3.3 22.2 - - - +
96C LEU* 4.0 13.1 - - + +
69D ARG* 3.3 58.8 - - + +
70D ILE* 3.5 17.5 - - + +
73D GLU* 4.1 11.7 - - + -
94D ALA 3.1 22.4 + - - +
95D VAL* 4.4 0.9 - - - +
96D ARG 3.5 0.2 - - - -
97D LEU* 1.3 76.5 - - - +
99D LEU* 1.3 75.5 + - + +
100D PRO* 3.9 5.4 - - - +
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Residues in contact with LEU 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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54C VAL* 4.4 2.5 - - + -
58C LEU* 4.0 32.5 - - + -
96C LEU* 4.2 19.5 - - + -
66D ILE* 5.3 5.6 - - + -
70D ILE* 5.6 4.0 - - + -
95D VAL* 3.0 28.6 + - + +
96D ARG 3.6 15.8 - - - +
97D LEU 4.7 0.7 - - - +
98D LEU* 1.3 90.6 - - + +
100D PRO* 1.3 66.5 - - + +
101D GLY 3.9 0.7 + - - -
103D LEU* 3.9 9.9 - - + +
104D ALA* 3.7 18.4 - - + +
107D ALA* 3.6 30.7 - - + -
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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