Contacts of the strand formed by residues 75 - 89 (chain D) in PDB entry 3M4D
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 LYS 75 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLU* 3.9 0.9 - - - +
71D GLU* 3.3 55.2 + - + +
72D GLY 3.1 17.8 + - - +
73D ALA 3.5 0.6 - - - -
74D ASN* 1.3 92.7 - - + +
76D SER* 1.3 64.7 + - - +
206D ALA* 3.6 2.2 - - - +
258D LEU 3.5 5.4 - - - +
259D HIS* 4.1 18.4 - - + -
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Residues in contact with SER 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL* 3.3 18.7 - - - +
69D SER* 2.9 23.1 + - - -
70D GLU* 4.3 0.9 - - - +
71D GLU* 4.9 1.8 - - - +
75D LYS* 1.3 78.4 - - - +
77D GLY* 1.3 58.1 + - - +
206D ALA* 3.6 6.1 - - - -
207D ALA* 3.3 31.5 - - - +
210D PHE* 3.4 8.8 - - - -
257D GLN* 3.5 6.4 - - - +
258D LEU 3.1 29.7 + - - +
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Residues in contact with GLY 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL* 3.3 11.1 - - - +
68D TYR* 3.1 44.7 + - - -
69D SER* 2.9 16.2 + - - -
76D SER* 1.3 75.8 + - - +
78D LEU* 1.3 60.4 + - - -
210D PHE* 3.9 2.9 - - - -
256D TYR 3.7 5.6 - - - -
257D GLN* 4.2 5.2 - - - -
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D TYR* 3.4 46.0 - - + +
66D ARG* 3.3 40.6 - - - +
67D VAL* 3.7 10.8 - - + +
68D TYR* 3.3 5.6 - - - -
77D GLY* 1.3 73.9 - - - +
79D ALA* 1.3 65.2 + - - +
80D TRP* 3.9 1.9 - - + -
196D PHE* 4.0 19.3 - - + -
210D PHE* 3.7 26.9 - - + -
254D ASP 3.7 0.5 - - - +
255D ASP* 3.6 2.6 - - - -
256D TYR* 2.8 46.6 + - + +
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Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLN 3.6 5.6 - - - +
65D TYR* 3.3 4.7 - - - -
66D ARG* 2.9 39.3 + - + +
68D TYR* 3.6 11.9 - - + -
78D LEU* 1.3 74.0 - - - +
80D TRP* 1.3 59.7 + - - +
253D ARG* 3.9 22.0 - - - +
254D ASP 3.4 6.1 - - - -
274D TRP* 3.5 25.4 - - + -
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Residues in contact with TRP 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLN 5.1 0.2 - - - -
65D TYR* 3.9 20.2 - - + -
78D LEU* 3.9 4.5 - - + -
79D ALA* 1.3 75.4 - - - +
81D PRO* 1.3 88.0 - - + +
82D SER* 3.3 13.8 + - - -
171D PHE* 3.5 34.3 - + - -
184D ARG* 3.6 28.0 - - + -
195D LEU* 3.8 15.9 - - + -
196D PHE* 3.5 23.1 - + + -
220D LEU* 3.7 11.4 - - + -
253D ARG* 3.1 7.2 - - - +
254D ASP* 2.8 66.5 + - + +
256D TYR* 3.8 14.2 - - + +
269D ASN* 2.9 24.0 + - - -
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Residues in contact with PRO 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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63D GLY 3.4 17.9 - - - +
65D TYR 4.4 1.1 - - - +
80D TRP* 1.3 97.1 - - + +
82D SER* 1.3 63.6 + - - +
83D ALA 3.3 1.6 - - - +
84D PHE* 3.6 31.0 - - + -
153D PHE* 3.8 8.7 - - - -
220D LEU* 3.3 49.5 - - + +
251D ARG* 4.0 9.6 - - + -
252D VAL 3.4 7.6 - - - +
253D ARG* 4.2 3.1 - - + -
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Residues in contact with SER 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D TRP* 3.3 19.9 + - - -
81D PRO* 1.3 73.6 - - - +
83D ALA* 1.3 62.0 + - - +
153D PHE* 4.7 0.9 - - - -
170D ILE* 3.6 2.4 - - - +
171D PHE* 2.8 27.2 + - - +
184D ARG* 3.7 18.5 + - - -
252D VAL* 2.8 18.0 + - - +
254D ASP* 2.7 38.3 + - - -
272D ASP* 3.8 6.2 + - - -
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Residues in contact with ALA 83 (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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81D PRO* 3.3 2.2 - - - +
82D SER* 1.3 84.8 - - - +
84D PHE* 1.3 67.2 + - - +
85D LYS* 5.2 7.6 - - + -
169D VAL 3.4 6.3 - - - -
170D ILE* 4.0 19.1 - - + -
250D GLU 4.1 0.2 - - - +
251D ARG* 3.4 4.7 - - - +
252D VAL* 2.8 51.4 + - + +
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Residues in contact with PHE 84 (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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61D ILE* 3.7 42.4 - - + -
62D ALA 3.9 11.2 - - - -
63D GLY* 4.2 0.4 - - - -
81D PRO* 3.6 24.0 - - + -
83D ALA* 1.3 77.6 - - - +
85D LYS* 1.3 61.7 + - - +
153D PHE* 3.8 25.4 - + - -
168D LYS* 3.3 3.5 - - - +
169D VAL* 2.7 47.5 + - + +
219D LEU* 3.3 31.2 - - + -
224D PHE* 3.8 40.2 - + + -
250D GLU 3.4 4.5 - - - +
251D ARG* 4.4 3.4 - - + -
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Residues in contact with LYS 85 (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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61D ILE* 3.9 2.5 - - - +
83D ALA* 5.2 9.6 - - + -
84D PHE* 1.3 81.9 - - - +
86D VAL* 1.3 69.1 + - - +
87D GLN* 3.7 24.9 - - + +
158D GLU* 2.8 27.5 + - - +
167D TRP 3.3 6.1 - - - +
168D LYS* 3.6 25.8 - - + +
170D ILE* 5.9 0.2 - - - -
228D PHE* 5.7 0.7 - - - -
248D ILE 4.3 1.1 - - - -
249D TYR* 3.4 1.4 - - - -
250D GLU* 2.8 67.3 + - + +
252D VAL* 5.5 4.0 - - + -
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D THR* 3.6 28.9 - - + +
61D ILE* 4.5 2.0 - - + -
85D LYS* 1.3 79.2 - - - +
87D GLN* 1.3 63.6 + - - +
88D LEU* 4.4 7.6 - - + -
166D GLY* 3.2 2.8 - - - -
167D TRP* 2.9 33.8 + - + -
224D PHE* 5.6 0.7 - - + -
226D PRO* 3.7 34.1 - - + -
228D PHE* 3.9 17.9 - - + -
247D VAL* 4.6 1.8 - - + -
248D ILE 3.2 4.7 - - - +
249D TYR* 3.9 28.7 - - + -
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Residues in contact with GLN 87 (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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85D LYS* 3.7 25.5 - - + +
86D VAL* 1.3 83.8 - - - +
88D LEU* 1.3 65.7 + - - +
89D GLN* 6.3 0.2 - - + -
158D GLU* 3.1 29.0 + - - +
164D LYS* 6.6 0.7 - - - -
165D VAL 3.5 8.1 - - - +
166D GLY* 4.4 0.9 - - - -
246D ASP 3.7 0.7 - - - +
247D VAL* 3.3 6.8 - - - +
248D ILE* 2.8 53.4 + - + +
250D GLU* 5.2 1.5 + - - -
277D ARG* 3.5 24.4 + - - +
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Residues in contact with LEU 88 (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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55D ILE* 4.0 24.2 - - + -
57D THR* 4.2 16.4 - - + -
86D VAL* 4.4 3.8 - - + -
87D GLN* 1.3 81.2 - - - +
89D GLN* 1.3 62.7 - - - +
98D ILE* 4.3 2.6 - - + +
163D LYS 4.0 0.4 - - - +
164D LYS* 3.3 4.5 - - - +
165D VAL* 2.8 41.6 + - + +
167D TRP* 3.8 16.4 - - + -
230D THR* 3.5 37.7 - - + +
245D ILE* 4.1 19.5 - - + -
246D ASP 3.3 4.5 - - - +
247D VAL* 4.1 19.1 - - + -
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Residues in contact with GLN 89 (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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87D GLN* 6.3 0.2 - - + -
88D LEU* 1.3 76.0 - - - +
90D LEU* 1.3 74.1 + - - +
91D PRO* 3.8 3.4 - - + +
92D ASP* 5.2 6.4 + - - +
163D LYS* 3.3 10.2 - - + +
164D LYS* 4.2 30.7 + - + +
245D ILE* 3.6 6.6 - - - +
246D ASP* 2.8 46.4 + - + +
248D ILE* 5.6 7.6 - - + +
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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