Contacts of the helix formed by residues 64 - 78 (chain D) in PDB entry 2I6A
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 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D ASN 3.2 24.2 - - - -
16D LEU* 3.9 3.8 + - - +
63D GLY* 1.3 73.0 - - - -
65D SER* 1.3 64.6 + - - -
66D THR 3.5 1.3 - - - -
67D GLN* 3.9 5.2 - - - -
68D ASN* 2.9 29.7 + - - -
500D 5I5 3.0 23.2 + - - -
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Residues in contact with SER 65 (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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14D ASN 4.6 0.6 + - - +
64D GLY* 1.3 70.3 - - - +
66D THR* 1.3 66.0 + - - +
68D ASN* 3.1 13.0 + - - +
69D SER* 3.2 15.7 + - - -
166D TYR* 4.8 5.1 + - - -
168D ALA* 4.2 9.7 - - - +
170D PHE* 3.7 34.9 - - - -
196D ASN* 5.4 2.8 + - - -
198D SER* 5.0 0.9 + - - -
300D ASP* 2.5 33.6 + - - +
500D 5I5 3.3 15.6 + - - -
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Residues in contact with THR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLY* 4.1 5.4 - - - -
12D MET 3.5 28.2 + - - +
13D GLY* 4.2 7.4 - - - -
14D ASN 5.7 1.0 + - - +
65D SER* 1.3 75.7 - - - +
67D GLN* 1.3 62.6 + - - +
69D SER* 3.3 1.9 + - - -
70D ILE* 3.0 23.9 + - + +
86D PHE* 4.1 6.7 - - + -
166D TYR* 3.3 46.4 - - + +
168D ALA* 2.8 31.1 + - - +
500D 5I5 5.7 0.4 - - - -
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Residues in contact with GLN 67 (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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14D ASN 5.5 0.4 + - - +
15D PRO* 3.5 18.7 - - - +
16D LEU 3.9 4.2 + - - +
63D GLY 2.3 38.7 + - - +
64D GLY* 3.9 5.1 - - - +
65D SER 3.1 0.4 - - - -
66D THR* 1.3 79.8 - - - +
68D ASN* 1.3 61.3 + - - +
70D ILE* 3.4 3.7 + - - +
71D LYS* 3.0 48.3 + - - +
86D PHE* 3.3 39.1 - - + -
99D LEU* 4.2 13.5 - - - +
103D ALA* 6.0 0.7 - - + -
112D TYR* 2.8 31.2 + - - +
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Residues in contact with ASN 68 (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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62D ALA 3.7 18.4 - - - +
63D GLY* 3.8 3.8 - - - +
64D GLY 2.9 20.9 + - - +
65D SER 3.1 4.9 + - - +
67D GLN* 1.3 75.9 - - - +
69D SER* 1.3 60.8 + - - +
71D LYS* 3.2 15.3 + - - +
72D VAL* 2.9 31.7 + - + +
297D GLY* 5.4 3.8 - - - -
300D ASP* 3.3 24.9 + - + +
332D ARG* 4.7 6.1 + - - +
500D 5I5 3.1 27.2 + - - +
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Residues in contact with SER 69 (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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65D SER 3.2 8.2 + - - -
66D THR 3.8 6.5 - - - -
68D ASN* 1.3 75.7 - - - +
70D ILE* 1.3 62.1 + - - +
72D VAL* 3.3 0.6 + - - -
73D ALA* 2.9 26.7 + - - +
166D TYR* 3.9 22.2 + - - -
300D ASP* 2.5 37.9 + - - -
303D VAL* 3.5 10.1 - - - +
304D GLY* 3.1 20.1 - - - -
307D LEU* 4.8 1.1 - - - -
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Residues in contact with ILE 70 (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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9D LEU* 3.4 30.3 - - + -
11D GLY* 4.0 31.9 - - - +
66D THR* 3.0 26.4 + - + +
67D GLN* 3.7 6.5 - - - +
68D ASN 3.2 0.2 - - - -
69D SER* 1.3 78.1 - - - +
71D LYS* 1.3 57.1 + - - +
73D ALA* 3.5 3.9 + - - +
74D GLN* 3.0 26.2 + - - +
84D ALA* 3.5 19.3 - - + +
85D THR 4.1 8.3 - - - +
86D PHE* 4.4 8.7 - - + -
108D VAL* 3.7 22.9 - - + -
166D TYR* 5.0 2.7 - - + -
307D LEU* 4.8 7.6 - - + -
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Residues in contact with LYS 71 (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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62D ALA* 3.4 32.9 + - - +
67D GLN* 3.0 37.4 + - - +
68D ASN* 3.5 14.7 + - - +
70D ILE* 1.3 75.7 - - - +
72D VAL* 1.3 57.8 + - + +
74D GLN* 3.1 2.9 + - - +
75D TRP* 2.8 30.1 + - - +
99D LEU 4.9 0.6 + - - -
102D LYS* 4.2 11.7 - - - +
103D ALA* 4.0 26.1 - - - +
106D ALA* 4.1 21.0 - - + +
108D VAL* 4.1 13.9 - - + -
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Residues in contact with VAL 72 (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 ASN* 2.9 19.8 + - + +
69D SER 3.9 3.6 - - - +
71D LYS* 1.3 78.4 - - + +
73D ALA* 1.3 56.0 + - - +
75D TRP* 3.5 7.4 + - + +
76D MET* 3.0 29.1 + - + +
301D ALA* 3.6 22.4 - - + +
304D GLY* 4.1 3.1 - - - -
305D GLY 3.7 7.0 - - - +
326D ALA* 3.6 30.3 - - + -
330D ILE* 3.8 38.8 - - + -
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Residues in contact with ALA 73 (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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9D LEU* 3.6 30.7 - - + -
69D SER 2.9 17.4 + - - +
70D ILE 3.7 2.5 - - - +
72D VAL* 1.3 72.5 - - - +
74D GLN* 1.3 62.5 + - - +
76D MET 3.4 0.2 + - - -
77D ILE* 2.9 37.6 + - + +
304D GLY* 3.3 22.8 + - - +
307D LEU* 4.1 7.0 - - + -
308D SER* 3.8 6.8 - - - +
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Residues in contact with GLN 74 (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 3.0 19.0 + - - +
71D LYS 3.7 3.6 - - - +
73D ALA* 1.3 75.8 - - - +
75D TRP* 1.3 58.3 + - - +
77D ILE* 3.8 4.4 - - - +
78D GLN* 2.9 33.2 + - - +
80D PRO 3.2 21.6 + - - -
81D HIS* 3.5 13.9 + - - +
82D LYS 3.6 0.2 + - - -
83D ALA* 2.6 31.9 + - - +
84D ALA* 2.9 17.3 + - + +
106D ALA 3.1 24.9 - - - +
107D HIS* 3.3 20.8 + - + +
108D VAL* 4.0 7.4 - - + -
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Residues in contact with TRP 75 (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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338A PHE* 5.6 1.0 - - + +
339A PRO* 2.9 34.5 + - + -
340A GLU* 3.0 20.5 + - - +
341A LYS 3.3 4.5 - - - -
342A PRO* 3.0 40.8 - - + +
71D LYS 2.8 16.4 + - - +
72D VAL* 3.6 8.7 - - + +
74D GLN* 1.3 77.5 - - - +
76D MET* 1.3 83.7 + - + +
78D GLN* 3.2 25.3 + - - +
106D ALA 5.1 1.8 + - - +
325D TYR* 3.8 14.6 - + - -
326D ALA* 5.0 2.7 - - - -
329D ILE* 3.9 15.5 - - + -
330D ILE* 4.3 26.9 - - + -
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Residues in contact with MET 76 (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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342A PRO* 3.2 42.0 - - + +
344A PHE* 3.0 35.2 - - + -
72D VAL* 3.0 22.8 + - + +
75D TRP* 1.3 91.5 - - + +
77D ILE* 1.3 65.6 + - - +
78D GLN* 3.9 1.4 - - - +
305D GLY* 4.3 7.9 - - - -
308D SER* 3.1 30.3 - - - +
309D GLN* 4.8 6.4 + - - +
322D ALA* 3.5 28.0 - - + +
325D TYR* 3.3 12.6 - - + -
326D ALA* 4.7 2.0 - - + -
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Residues in contact with ILE 77 (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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4D VAL* 4.2 10.1 - - + -
8D ILE* 5.1 4.3 - - + -
9D LEU* 5.2 8.1 - - + -
73D ALA* 2.9 30.3 + - + +
74D GLN* 3.8 4.7 - - - +
76D MET* 1.3 75.5 - - - +
78D GLN* 1.3 57.1 + - - +
79D GLN* 2.4 31.0 + - + +
80D PRO* 3.8 19.3 - - + +
83D ALA* 3.7 34.3 - - + -
84D ALA* 5.5 0.4 - - + +
308D SER* 3.9 24.2 - - - +
309D GLN* 6.0 0.9 - - - +
311D VAL* 4.3 20.4 - - + -
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Residues in contact with GLN 78 (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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340A GLU 3.6 8.1 - - - +
341A LYS* 2.3 54.6 - - + +
342A PRO* 4.0 10.7 - - + +
74D GLN* 2.9 18.8 + - - -
75D TRP* 3.2 22.1 - - - +
76D MET 3.2 4.4 - - - +
77D ILE* 1.3 78.3 - - - +
79D GLN* 1.3 74.6 + - - +
80D PRO 4.2 2.8 - - - +
81D HIS* 4.0 23.1 + - - -
107D HIS* 5.5 5.1 - - - -
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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