Contacts of the strand formed by residues 74 - 82 (chain D) in PDB entry 6QPA
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 MET 74 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D LYS* 3.4 3.8 - - - -
15D ILE* 3.0 48.4 + - + +
16D ALA 4.7 2.0 - - - +
17D ASN* 3.6 29.6 - - + +
22D TYR* 3.6 28.9 - - - +
25D MET* 6.1 0.2 - - - -
49D LEU* 3.9 25.4 - - + -
50D GLN 3.2 24.0 - - - +
68D ARG* 5.0 9.0 - - + +
71D LEU* 4.0 23.1 - - + +
72D ASN* 4.1 0.6 - - - +
73D PRO* 1.3 75.2 - - - +
75D GLY* 1.3 63.7 + - - +
76D MET 3.6 0.3 + - - -
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Residues in contact with GLY 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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13D ALA 3.5 7.4 - - - -
14D LYS* 4.4 12.6 - - - +
49D LEU* 3.7 4.3 - - - +
50D GLN* 2.8 56.2 + - - +
74D MET* 1.3 75.2 - - - +
76D MET* 1.3 58.1 + - - +
77D PHE* 4.9 2.9 - - - -
297D MET* 4.6 6.1 - - - -
299D PHE* 4.4 4.0 - - - -
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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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11D ASN* 3.5 3.3 - - - +
13D ALA* 2.7 43.5 + - + +
15D ILE* 4.0 24.5 - - + -
25D MET* 4.1 21.5 - - + +
47D GLN* 4.4 12.3 - - + +
48D LEU 3.4 6.5 - - - +
49D LEU* 3.7 23.3 - - + -
75D GLY* 1.3 71.9 - - - +
77D PHE* 1.3 63.1 + - - +
78D GLN* 3.5 38.5 - - - +
109D MET* 4.3 19.3 - - + -
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Residues in contact with PHE 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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10D ILE* 3.8 22.9 - - + -
11D ASN 3.2 3.1 - - - -
12D MET* 3.7 42.2 - - + -
13D ALA 4.6 4.0 - - - -
14D LYS* 5.8 3.6 - - + -
46D GLU 3.5 1.7 - - - +
47D GLN* 3.8 0.9 - - - -
48D LEU* 2.8 52.2 + - + +
75D GLY* 4.2 1.5 - - - -
76D MET* 1.3 86.7 - - - +
78D GLN* 1.3 62.3 + - - +
79D TYR* 4.0 1.6 - + + -
162D ILE* 3.7 30.3 - - + -
254D LEU* 5.0 2.7 - - + -
297D MET* 4.3 19.3 - - + -
299D PHE* 3.8 24.2 - + + -
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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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9D ALA 3.3 2.4 - - - +
10D ILE* 3.4 0.2 - - - -
11D ASN* 2.8 56.1 + - + +
29D GLY* 6.0 3.0 - - - -
32D VAL* 4.8 14.8 - - - +
33D CSS 4.8 12.4 - - - -
46D GLU 3.4 4.3 - - - +
47D GLN* 4.3 22.3 - - + +
76D MET* 3.5 35.3 - - - +
77D PHE* 1.3 76.4 - - - +
79D TYR* 1.3 65.7 + - - +
80D THR* 3.6 7.9 + - + +
103D CSS 5.7 6.9 - - - -
106D CYS* 6.3 0.4 - - - -
116D GLU* 5.2 0.3 - - - +
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Residues in contact with TYR 79 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D ILE* 4.0 23.1 - - + -
9D ALA 3.4 5.2 - - - -
10D ILE* 3.6 36.1 - - + -
45D PHE* 3.0 11.0 - - - +
46D GLU* 2.8 52.6 + - + +
48D LEU* 3.7 23.3 - - + +
77D PHE* 4.6 2.7 - - + -
78D GLN* 1.3 73.1 - - - +
80D THR* 1.3 60.9 + - - +
81D VAL* 4.7 4.3 - - + -
162D ILE* 3.5 18.6 - - + +
197D MET* 4.2 11.7 - - + -
199D MET* 3.5 15.6 - - + +
256D HIS* 2.9 37.7 + + - -
308D TRP* 4.9 3.8 - + - -
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Residues in contact with THR 80 (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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8D ILE* 3.6 1.6 - - - -
9D ALA* 2.8 45.6 + - - +
33D CSS 4.3 13.9 - - - -
36D THR* 4.3 8.5 - - + +
42D PHE* 4.1 16.2 - - + -
44D GLY 3.5 3.1 - - - -
45D PHE* 4.2 5.8 - - + -
78D GLN* 3.6 8.6 + - + +
79D TYR* 1.3 79.1 - - - +
81D VAL* 1.3 61.6 + - - +
82D TRP* 2.9 31.9 + - + -
88D HIS* 3.9 6.8 + - - -
116D GLU* 4.1 4.6 + - - +
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Residues in contact with VAL 81 (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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6D PRO* 3.6 31.6 - - + -
7D ILE 3.4 7.4 - - - +
8D ILE* 4.2 19.3 - - + -
42D PHE* 3.8 1.9 - - - -
43D LEU* 2.8 31.8 + - + -
44D GLY 2.8 19.2 + - - +
45D PHE 4.8 0.2 - - - +
79D TYR* 4.7 6.1 - - + -
80D THR* 1.3 76.6 - - - +
82D TRP* 1.3 64.9 + - - +
308D TRP* 3.7 50.9 - - + +
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Residues in contact with TRP 82 (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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6D PRO* 3.4 4.5 - - - +
7D ILE* 2.9 38.4 + - + +
9D ALA* 4.4 5.6 - - + -
36D THR* 3.4 35.4 - - + -
39D HIS* 4.0 6.5 - - + -
41D GLY 3.3 22.7 - - - -
42D PHE* 3.7 22.4 - + + -
43D LEU* 3.6 6.3 - - - -
80D THR* 2.9 44.6 + - + -
81D VAL* 1.3 74.8 - - - +
83D LYS* 1.3 62.3 + - - +
84D ASP 3.2 19.2 + - - +
87D SER* 3.8 23.6 - - - -
88D HIS* 3.2 38.5 - + + -
91D MET* 3.6 24.7 - - + -
118D TYR* 5.6 1.1 - + - -
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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