Contacts of the strand formed by residues 77 - 87 (chain D) in PDB entry 1QQW
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 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ARG* 4.3 9.0 - - - +
175A HIS* 5.8 1.8 - - + -
75D HIS 3.6 0.2 - - - -
76D ALA* 1.3 76.7 - - - +
78D GLY* 1.3 61.2 + - - +
114D SER* 3.3 3.2 - - - -
115D THR* 3.3 34.6 + - + +
118D GLY 3.9 2.4 + - - -
119D GLU 3.6 5.8 - - - +
120D SER* 3.3 27.4 - - - +
122D SER* 3.1 36.8 + - - +
123D ALA 5.6 0.2 - - - +
124D ASP* 3.2 22.1 + - - +
258D PRO* 3.0 22.6 + - - +
259D ASP* 2.5 34.3 + - - +
262D ILE* 4.1 12.3 - - + +
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Residues in contact with GLY 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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76D ALA 3.3 5.9 + - - -
77D LYS* 1.3 76.8 - - - +
79D ALA* 1.3 59.9 + - - +
112D ARG* 3.9 11.9 - - - +
113D PHE 2.9 14.6 - - - -
114D SER* 3.8 4.3 - - - -
124D ASP* 5.7 1.8 - - - -
209D HIS* 5.5 1.6 - - - -
262D ILE* 3.9 15.8 - - - +
325D TYR* 2.7 27.9 + - - -
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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
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78D GLY* 1.3 74.9 - - - +
80D GLY* 1.3 61.0 + - - +
112D ARG* 3.0 10.3 - - - +
113D PHE* 2.7 31.6 + - - -
209D HIS* 4.1 23.8 - - + +
262D ILE* 3.9 28.5 - - + +
265D LEU* 4.4 9.4 - - + -
325D TYR* 4.4 7.0 - - - -
329D VAL* 4.3 1.6 - - - -
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Residues in contact with GLY 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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79D ALA* 1.3 76.8 - - - +
81D ALA* 1.3 65.3 + - - +
111D VAL 3.2 10.1 - - - -
112D ARG* 4.2 1.8 - - - -
113D PHE* 5.3 0.4 - - - -
265D LEU* 3.9 10.0 - - - +
321D ASN* 5.0 1.6 + - - -
322D PRO* 3.6 21.0 - - - +
325D TYR* 4.7 1.6 - - - -
329D VAL* 3.7 24.5 - - - +
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D GLY* 1.3 76.6 - - - +
82D PHE* 1.3 75.8 + - - +
111D VAL* 3.0 31.4 + - - +
113D PHE* 4.9 0.9 - - + -
265D LEU* 4.0 12.1 - - + -
269D ILE* 3.7 27.4 - - + -
318D LEU* 4.0 18.8 - - + -
320D ARG 3.7 5.2 - - - -
321D ASN* 5.0 0.2 - - - +
322D PRO* 4.6 2.6 - - - +
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Residues in contact with PHE 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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81D ALA* 1.3 82.7 - - - +
83D GLY* 1.3 59.4 + - - +
109D ILE 3.8 15.7 - - - +
110D ALA* 3.8 20.6 - - + -
137D TYR* 4.5 5.2 - + - -
318D LEU* 3.1 12.2 - - - +
319D ASN* 2.8 21.0 + - - -
320D ARG* 2.8 63.6 + - - +
321D ASN 4.2 2.7 - - - -
322D PRO* 3.9 18.2 - - + -
328D GLU* 3.6 47.1 - - + -
329D VAL* 5.5 1.1 - - + -
332D ILE* 5.1 0.9 - - + -
375D VAL* 4.1 14.4 - - + -
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Residues in contact with GLY 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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82D PHE* 1.3 78.6 - - - +
84D TYR* 1.3 66.4 + - - +
108D PRO* 3.8 5.5 - - - +
109D ILE* 3.3 23.8 + - - +
317D VAL 3.0 14.4 - - - -
319D ASN* 3.4 18.2 - - - -
320D ARG* 5.0 2.5 + - - +
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Residues in contact with TYR 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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83D GLY* 1.3 79.1 - - - +
85D PHE* 1.3 62.7 + - - +
86D GLU* 3.6 23.9 + - + -
106D LYS* 3.4 45.5 + - + -
107D THR 3.4 15.0 - - - +
108D PRO* 4.4 1.8 - - + -
109D ILE* 3.2 15.3 - - - +
315D LYS 4.1 0.5 - - - +
316D LEU* 4.0 0.5 - - - -
317D VAL* 3.0 67.5 + - + +
319D ASN* 4.4 17.0 - - - -
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Residues in contact with PHE 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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84D TYR* 1.3 75.1 - - - +
86D GLU* 1.3 70.9 + - - +
87D VAL* 3.9 21.8 - - + -
99D VAL* 3.9 21.8 - - + -
100D PHE* 3.9 29.8 - + - -
105D LYS 3.4 2.6 - - - +
106D LYS* 3.1 6.2 - - - -
107D THR* 2.8 39.7 + - - +
109D ILE* 3.8 3.1 - - + -
136D PHE* 3.6 26.5 - + + -
279D PHE* 4.0 29.2 - + + -
313D VAL* 4.3 12.3 - - + -
314D GLY* 4.4 1.8 - - - -
315D LYS 3.2 24.5 - - - -
316D LEU* 3.4 15.3 - - + -
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Residues in contact with GLU 86 (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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84D TYR* 3.6 22.8 + - + -
85D PHE* 1.3 78.8 - - - +
87D VAL* 1.3 71.9 + - - +
88D THR* 3.5 7.8 + - + +
104D GLY* 4.2 16.3 - - - +
105D LYS 3.7 1.8 - - - -
106D LYS* 3.2 35.0 + - + +
314D GLY* 3.1 4.2 - - - -
315D LYS* 2.8 48.5 + - + +
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Residues in contact with VAL 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 PHE* 3.9 12.6 - - + -
86D GLU* 1.3 75.6 - - - +
88D THR* 1.3 59.6 + - - +
89D HIS 3.3 24.5 - - - +
90D ASP* 5.1 0.9 - - - -
99D VAL 3.3 27.1 - - - +
100D PHE* 3.9 23.8 - - + +
102D HIS 3.6 22.2 - - - +
103D ILE* 3.7 9.9 - - + +
104D GLY* 2.7 28.6 + - - +
105D LYS* 3.4 14.4 + - + +
313D VAL* 3.8 8.3 - - + +
314D GLY* 4.3 0.7 - - - -
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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