Contacts of the strand formed by residues 42 - 53 (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 PHE 42 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D CSS 4.8 3.1 - - - -
36D THR* 3.4 37.5 - - + +
37D ALA* 3.6 30.3 - - + -
39D HIS 2.9 17.2 + - - +
40D PRO 3.2 3.5 - - - +
41D GLY* 1.3 75.6 - - - +
43D LEU* 1.3 63.9 + - - +
44D GLY* 3.3 39.0 - - - -
45D PHE* 3.8 19.7 - + + -
80D THR* 4.1 11.7 - - + -
81D VAL 3.9 4.9 - - - -
82D TRP* 3.7 22.5 - + + -
305D GLN* 4.2 11.8 + - + -
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Residues in contact with LEU 43 (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 GLU* 4.5 4.9 - - - +
6D PRO* 3.6 31.4 - - + -
40D PRO 5.2 0.7 - - - +
41D GLY 3.7 8.1 - - - +
42D PHE* 1.3 79.3 - - - +
44D GLY* 1.3 55.5 + - - +
81D VAL* 2.8 15.5 + - + +
82D TRP* 3.6 14.8 - - - +
83D LYS* 3.6 31.6 - - + +
305D GLN* 3.6 11.0 + - - +
307D LEU* 4.1 3.6 - - - +
308D TRP* 3.3 33.1 + - + -
311D HIS* 3.7 31.1 + - + +
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Residues in contact with GLY 44 (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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42D PHE* 3.3 16.3 - - - -
43D LEU* 1.3 79.7 - - - +
45D PHE* 1.3 61.4 + - - +
81D VAL* 2.8 26.9 + - - +
305D GLN* 3.4 24.7 - - - -
308D TRP* 3.9 10.1 - - - -
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Residues in contact with PHE 45 (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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33D CSS 3.9 45.3 - - + -
42D PHE* 3.8 21.5 - + + -
44D GLY* 1.3 75.0 - - - +
46D GLU* 1.3 75.5 + - - +
47D GLN* 4.1 6.1 - - + -
79D TYR 3.0 17.5 - - - +
80D THR* 4.2 2.0 - - + -
81D VAL* 4.9 0.9 - - - -
303D MET* 3.7 42.4 - - + -
304D GLU 4.3 2.0 - - - -
305D GLN* 3.1 59.9 + - + +
308D TRP* 4.1 1.3 - - - +
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Residues in contact with GLU 46 (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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45D PHE* 1.3 82.3 - - - +
47D GLN* 1.3 59.4 + - - +
48D LEU* 3.7 15.4 + - + +
77D PHE 3.5 2.8 - - - +
78D GLN* 3.4 4.1 - - - -
79D TYR* 2.8 63.6 + - + -
158D ARG* 4.4 0.5 + - - -
160D VAL* 6.1 0.7 - - - +
256D HIS* 5.7 2.7 - - + -
301D PRO* 4.8 3.1 - - - +
303D MET 3.9 1.8 - - - -
304D GLU* 2.6 36.3 - - - +
306D GLY* 4.6 3.5 - - - -
308D TRP* 3.0 35.0 + - + +
309D ARG* 3.3 19.5 + - - -
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Residues in contact with GLN 47 (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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25D MET* 4.4 27.0 + - - +
29D GLY* 4.8 5.1 - - - -
45D PHE* 4.1 5.3 - - + -
46D GLU* 1.3 71.4 - - - +
48D LEU* 1.3 58.6 + - - +
49D LEU* 6.3 0.2 - - + -
76D MET* 4.4 13.2 - - + +
77D PHE 3.8 1.8 - - - -
78D GLN* 4.3 30.3 - - + +
301D PRO* 3.3 4.5 - - - +
302D MET* 2.8 50.0 + - + +
303D MET* 3.0 64.0 + - + +
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Residues in contact with LEU 48 (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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46D GLU* 4.3 17.7 - - + +
47D GLN* 1.3 75.7 - - - +
49D LEU* 1.3 59.4 + - - +
76D MET* 3.4 8.2 - - - +
77D PHE* 2.8 46.6 + - + +
79D TYR* 3.7 38.4 - - + +
160D VAL* 4.1 28.5 - - + -
162D ILE* 4.0 15.3 - - + -
256D HIS* 5.0 1.6 - - + -
299D PHE* 3.6 16.6 - - + -
300D SER 3.5 1.6 - - - -
301D PRO* 3.8 28.7 - - + -
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Residues in contact with LEU 49 (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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15D ILE* 4.4 2.0 - - + -
22D TYR* 3.6 32.3 - - + +
25D MET* 4.4 14.6 - - + -
47D GLN* 4.1 0.6 + - + -
48D LEU* 1.3 72.6 - - - +
50D GLN* 1.3 64.9 + - - +
51D THR* 3.4 5.0 + - + +
74D MET* 3.9 30.3 - - + -
75D GLY 3.8 9.2 - - - +
76D MET* 3.7 23.6 - - + -
299D PHE* 3.6 2.2 - - - -
300D SER* 2.7 38.0 + - - +
302D MET* 3.9 32.1 - - + -
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Residues in contact with GLN 50 (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 LYS* 4.4 4.9 + - - -
49D LEU* 1.3 72.7 - - - +
51D THR* 1.3 63.7 + - - +
52D GLY 3.1 19.7 + - - +
53D ILE* 3.6 17.2 - - - +
68D ARG* 5.1 0.2 - - - +
71D LEU* 3.5 27.1 - - + +
73D PRO 5.1 0.3 - - - +
74D MET* 3.2 26.3 - - - +
75D GLY* 2.8 45.7 + - - +
295D TYR* 5.4 0.6 + - - -
297D MET* 3.3 29.0 - - + +
298D PHE 3.3 13.9 - - - +
299D PHE* 3.5 10.8 - - + -
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Residues in contact with THR 51 (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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49D LEU* 3.8 5.2 - - + +
50D GLN* 1.3 77.9 - - - +
52D GLY* 1.3 52.6 + - - +
65D VAL 3.4 6.8 + - - +
66D ASP* 3.6 2.3 - - - -
67D MET* 2.7 32.1 + - - -
68D ARG* 3.5 33.1 + - + +
71D LEU* 4.5 4.9 - - - -
159D THR* 5.7 0.9 - - - +
262D PRO* 5.6 5.7 - - - +
298D PHE* 2.8 26.7 + - - +
299D PHE* 3.9 2.9 + - - -
300D SER* 3.8 29.2 - - - -
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Residues in contact with GLY 52 (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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50D GLN* 3.1 20.3 + - - +
51D THR* 1.3 82.4 + - - +
53D ILE* 1.3 64.7 + - - +
64D ALA 3.5 5.4 - - - -
65D VAL 3.2 10.5 - - - -
67D MET* 4.0 13.2 - - - -
71D LEU* 4.6 0.2 - - - -
298D PHE* 2.8 23.4 + - - +
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Residues in contact with ILE 53 (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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50D GLN* 3.6 15.3 - - - +
52D GLY* 1.3 79.3 - - - +
54D HIS* 1.3 65.6 + - - +
55D PRO* 3.4 1.9 - - - +
60D TYR* 3.7 28.0 - - + +
63D GLY* 3.6 22.7 - - - -
64D ALA 3.0 32.7 + - - +
65D VAL* 3.3 15.1 + - - +
67D MET* 4.2 8.5 - - + -
71D LEU* 6.2 0.2 - - + -
295D TYR* 3.3 34.1 - - + +
296D TYR 3.3 13.5 - - - +
297D MET* 4.5 0.9 - - - -
298D PHE* 3.7 8.2 - - - -
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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