Contacts of the strand formed by residues 83 - 90 (chain D) in PDB entry 6ULG
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 ARG 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D LEU* 3.5 36.5 - - - +
20D VAL* 4.0 15.9 - - + +
21D LEU 3.5 8.1 - - - +
22D SER* 4.2 13.1 - - - -
27D LEU* 4.3 21.0 - - - +
79D VAL* 4.1 2.0 - - - +
80D SER* 2.8 42.9 + - - +
81D GLY 4.9 0.2 - - - -
82D GLN* 1.3 106.8 - - + +
84D VAL* 1.3 60.5 + - - +
85D PHE* 4.9 2.0 - - + -
108E LEU* 6.3 0.4 - - - -
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Residues in contact with VAL 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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20D VAL* 3.3 2.4 - - - +
21D LEU* 2.5 70.3 + - + +
23D GLU 5.9 0.4 - - - +
43D ILE* 6.0 2.2 - - + -
44D SER* 5.9 3.6 - - - -
47D VAL* 4.2 20.2 - - + -
77D VAL* 3.7 23.3 - - + -
78D THR 3.6 14.6 - - - +
79D VAL* 3.8 18.4 - - + +
83D ARG* 1.3 74.9 - - - +
85D PHE* 1.3 65.1 + - - +
108E LEU* 5.0 9.4 - - + -
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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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5D LEU* 4.3 27.6 - - + -
9D LEU* 3.8 33.2 - - + -
19D LEU 3.5 4.0 - - - -
20D VAL* 3.6 33.7 - - + -
21D LEU* 6.3 0.4 - - - -
76D LEU 4.5 0.2 - - - -
77D VAL* 3.2 31.4 - - - +
78D THR 3.2 16.3 + - - +
80D SER* 3.2 28.3 - - - -
83D ARG* 4.8 4.0 - - + -
84D VAL* 1.3 76.5 - - - +
86D VAL* 1.3 61.3 + - - +
115E PRO* 4.3 20.4 - - + -
116E HIS* 4.5 12.3 - + - -
119E LEU* 4.1 17.0 - - + -
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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
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9D LEU* 5.1 1.4 - - - +
18D TYR* 3.3 0.7 - - - +
19D LEU* 2.8 61.0 + - + +
21D LEU* 6.5 0.4 - - + -
33D LEU* 3.9 13.5 - - + -
43D ILE* 4.7 21.8 - - + -
75D LEU* 4.3 26.5 - - + -
76D LEU 3.3 17.9 - - - +
77D VAL* 4.1 9.9 - - + -
85D PHE* 1.3 75.4 - - - +
87D VAL* 1.3 72.6 + - - +
119E LEU* 4.4 0.7 - - - -
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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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9D LEU* 3.8 24.2 - - + -
12D ILE* 4.4 19.1 - - + -
15D GLN* 4.5 9.2 - - + -
17D GLY 3.3 4.9 - - - +
18D TYR* 3.9 7.4 - - + -
75D LEU* 3.5 2.7 - - - -
76D LEU* 3.1 31.3 + - + +
86D VAL* 1.3 81.6 - - - +
88D LYS* 1.3 70.2 + - - +
89D ARG* 3.7 22.6 + - + +
119E LEU* 3.7 30.5 - - + -
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Residues in contact with LYS 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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14D ASP 3.7 0.3 - - - +
15D GLN* 3.6 4.3 - - - -
16D LEU* 2.8 43.1 + - + -
17D GLY* 2.4 32.9 + - - +
32D ASP* 2.8 53.7 + - + +
33D LEU* 3.7 20.5 - - + +
73D HIS* 3.4 42.1 + - + +
74D THR 3.3 5.2 - - - +
75D LEU* 4.3 13.5 - - + +
86D VAL* 4.4 0.4 - - - +
87D VAL* 1.3 68.8 - - - +
89D ARG* 1.3 60.3 + - - +
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Residues in contact with ARG 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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12D ILE* 4.5 2.0 - - + +
14D ASP* 2.7 46.0 + - - +
16D LEU* 4.3 4.5 - - - -
73D HIS* 3.3 6.6 - - - +
74D THR* 2.7 54.2 + - + +
76D LEU* 4.1 20.4 - - + +
87D VAL* 3.7 17.9 + - + +
88D LYS* 1.3 77.4 - - - +
90D GLN* 1.3 59.8 - - - +
92D ARG* 3.2 22.2 - - - +
119E LEU 2.8 34.6 + - - -
120E ALA* 3.6 8.1 + - - +
121E SER 2.7 29.2 + - - -
122E GLU 5.1 0.2 - - - -
123E PRO* 3.4 24.3 - - - +
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Residues in contact with GLN 90 (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 ASP* 3.4 31.3 + - + +
16D LEU* 3.7 29.7 - - + +
72D GLU 4.0 9.4 - - - +
73D HIS* 5.4 0.2 - - + -
74D THR* 5.2 1.2 - - - +
89D ARG* 1.3 75.2 - - - +
91D ASN* 1.3 82.5 + - - +
92D ARG* 3.8 9.9 + - - +
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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