Contacts of the strand formed by residues 81 - 90 (chain Q) in PDB entry 3QUM
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 GLN 81 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C PHE* 3.6 7.4 - - - -
50C ARG* 4.9 1.3 - - - +
65Q ILE 4.6 0.2 - - - -
66Q LEU* 3.7 1.9 - - - -
67Q LEU* 3.3 36.4 + - + +
79Q THR* 4.8 6.9 + - - +
80Q GLY* 1.3 76.0 - - - +
82Q VAL* 1.3 68.8 + - - +
83Q PHE* 3.8 12.0 - - + -
112Q ALA* 3.3 15.0 - - - +
113Q GLU* 3.0 51.2 + - - +
115Q THR* 3.1 19.8 + - - +
118Q VAL* 3.7 14.4 - - + +
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Residues in contact with VAL 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C PHE* 4.2 20.2 - - + -
32C PHE* 4.1 23.3 - - + -
50C ARG* 4.2 18.6 - - - +
97D ARG* 3.3 24.0 + - + +
98D LEU* 3.7 30.3 - - + -
64Q VAL* 4.8 1.6 - - + -
65Q ILE 3.4 11.2 - - - +
66Q LEU* 4.6 5.4 - - + -
81Q GLN* 1.3 81.1 - - - +
83Q PHE* 1.3 87.7 + - - +
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Residues in contact with PHE 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLY 4.3 6.5 - - - -
97D ARG* 3.6 31.0 - - + +
98D LEU* 5.9 0.2 - - - -
64Q VAL* 3.3 4.3 - - - -
65Q ILE* 2.7 38.9 + - + +
67Q LEU* 4.2 11.4 - - + -
81Q GLN* 3.8 16.6 - - + -
82Q VAL* 1.3 96.9 - - - +
84Q GLN* 1.3 64.8 + - - +
108Q LEU* 3.9 30.5 - - + -
109Q SER* 4.4 1.8 - - - +
110Q GLU* 4.0 24.9 - - + -
111Q PRO 4.2 1.6 - - - -
112Q ALA* 3.2 44.9 - - + -
113Q GLU 4.6 1.1 - - - -
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Residues in contact with GLN 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D TRP* 2.8 57.1 - - + +
95D SER* 2.5 42.0 + - - +
96D GLY* 2.7 23.9 + - - +
97D ARG* 2.9 4.9 + - - +
98D LEU* 3.5 14.0 + - + +
63Q SER 3.9 4.5 - - - -
64Q VAL* 4.0 11.4 - - + +
83Q PHE* 1.3 76.3 - - - +
85Q VAL* 1.3 62.5 + - - +
86Q SER 3.8 0.2 - - - -
108Q LEU* 3.7 6.2 - - - +
109Q SER* 3.4 27.2 + - - +
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Residues in contact with VAL 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D TRP* 2.6 20.6 - - + -
52D ASN* 3.8 4.0 - - - +
33Q VAL* 5.7 0.4 - - + -
61Q ASN 5.5 1.9 - - - +
63Q SER* 2.5 57.3 + - - +
64Q VAL* 3.7 7.9 - - - +
65Q ILE* 4.5 10.5 - - + -
84Q GLN* 1.3 70.0 - - - +
86Q SER* 1.3 62.6 + - - +
87Q HIS* 3.2 26.9 - - - +
88Q SER* 4.7 4.9 - - - +
106Q LEU* 4.2 20.9 - - + -
107Q ARG 4.0 6.1 - - - +
108Q LEU* 4.7 2.0 - - - +
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Residues in contact with SER 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D SER 3.8 3.4 - - - -
31D SER* 3.3 33.9 - - - -
33D TRP* 3.5 11.5 - - - -
52D ASN* 3.2 25.5 + - - +
53D SER* 3.8 3.4 - - - -
54D THR* 3.6 5.0 - - - +
84Q GLN 3.5 4.9 + - - -
85Q VAL* 1.3 71.0 - - - +
87Q HIS* 1.3 60.7 + - - +
107Q ARG* 2.4 47.4 + - - -
109Q SER 4.3 6.5 - - - -
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Residues in contact with HIS 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D SER* 3.2 35.2 + - - +
54D THR* 3.3 20.4 - - + +
85Q VAL* 3.2 15.4 - - - +
86Q SER* 1.3 87.4 + - - +
88Q SER* 1.3 75.6 + - - +
89Q PHE* 2.9 43.8 - + + -
106Q LEU* 3.8 0.2 - - - -
107Q ARG* 3.1 34.9 + - + +
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Residues in contact with SER 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D THR* 5.9 1.2 - - - +
59Q ILE* 4.7 11.8 - - - +
60Q ARG 4.9 6.4 + - - -
85Q VAL* 4.7 4.5 - - - +
87Q HIS* 1.3 95.8 + - - +
89Q PHE* 1.3 66.5 + - - +
90Q PRO* 4.0 6.0 - - - +
104Q MET* 4.1 9.4 - - - -
105Q LEU 3.4 6.5 - - - -
106Q LEU* 3.7 21.3 - - - -
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Residues in contact with PHE 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Q TRP* 3.3 39.9 - + - -
87Q HIS* 2.9 43.3 - + + -
88Q SER* 1.3 74.9 - - - +
90Q PRO* 1.3 67.5 - - + +
104Q MET* 3.2 4.5 - - - +
105Q LEU* 2.9 52.7 + - + -
107Q ARG* 4.3 9.0 - - + -
237Q TRP* 3.9 12.7 - - + -
241Q THR* 5.6 8.7 - - - -
245Q ASN* 4.0 27.4 - - + -
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Residues in contact with PRO 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Q ALA* 3.7 18.8 - - + -
59Q ILE* 3.8 21.8 - - + -
88Q SER 4.0 5.2 - - - +
89Q PHE* 1.3 89.2 - - + +
91Q HIS* 1.3 69.4 + - - +
92Q PRO* 3.2 8.1 - - - +
94Q TYR* 5.9 1.6 - - + -
95Q MET* 4.8 14.1 - - - +
104Q MET* 4.0 8.5 - - + -
237Q TRP* 4.2 3.4 - - - -
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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