Contacts of the strand formed by residues 76 - 86 (chain I) in PDB entry 2QC8
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 ASP 76 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61I ASN* 4.0 17.1 + - + +
62I PHE 3.3 9.2 - - - -
74I ASN 4.7 0.5 - - - +
75I SER* 1.3 74.1 - - - +
77I MET* 1.3 62.2 + - - +
104I TYR* 4.5 4.9 + - - +
317J ALA* 3.3 16.9 - - - +
319J ARG* 2.9 17.4 + - - +
324J ARG* 3.1 31.7 + - - -
326J PRO* 3.7 0.9 - - - +
327J ARG* 3.0 61.7 + - + +
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Residues in contact with MET 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I ASN* 2.9 27.1 - - - +
62I PHE* 3.0 32.3 + - + +
64I GLY* 3.7 11.7 - - - -
69I GLN* 3.6 42.4 - - + +
70I SER* 3.9 6.7 - - - +
75I SER 3.4 13.7 - - - +
76I ASP* 1.3 74.0 - - - +
78I TYR* 1.3 65.5 + - - +
101I VAL* 4.0 11.2 - - + -
102I PHE 3.5 16.8 - - - +
103I LYS* 3.7 28.9 - - + -
104I TYR 5.1 1.1 - - - +
109I ALA* 4.2 8.7 - - + -
110I GLU* 5.5 0.4 - - - +
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Residues in contact with TYR 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I GLU* 4.1 19.7 - - - -
60I TRP 3.6 8.1 - - - +
61I ASN* 4.3 3.6 - - + +
77I MET* 1.3 76.3 - - - +
79I LEU* 1.3 66.2 + - - +
80I VAL* 4.1 0.9 - - + -
100I GLU 3.5 0.4 - - - +
101I VAL* 3.4 10.4 - - - +
102I PHE* 2.9 44.7 + - + +
103I LYS 3.1 28.0 - - - -
104I TYR 3.8 5.2 + - - -
106I ARG* 3.8 41.8 - - + +
327J ARG* 3.1 40.5 - - + +
328J THR* 5.6 7.6 - - - -
331J GLN* 3.8 18.4 - - + +
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Residues in contact with LEU 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I TYR* 4.2 19.5 - - + -
32I TRP* 3.7 50.9 - - + -
43I LYS* 4.7 3.6 - - - -
59I GLU* 3.4 8.4 - - - +
60I TRP* 2.6 43.4 + - + +
61I ASN* 3.9 16.8 - - - +
62I PHE* 3.4 36.6 - - + -
78I TYR* 1.3 73.8 - - - +
80I VAL* 1.3 62.4 + - - +
81I PRO* 3.7 2.8 - - - +
99I CYS* 4.0 17.0 - - + -
100I GLU 3.5 1.6 - - - +
101I VAL* 4.1 4.3 - - + -
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Residues in contact with VAL 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I GLU* 4.2 13.9 - - + +
78I TYR* 5.0 2.2 - - + -
79I LEU* 1.3 73.3 - - - +
81I PRO* 1.3 82.3 - - + +
82I ALA* 4.4 0.2 - - - +
99I CYS* 4.1 2.4 - - - +
100I GLU* 2.9 29.9 + - + +
102I PHE* 3.5 35.9 - - + -
106I ARG* 3.7 21.1 - - - +
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Residues in contact with PRO 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I TYR* 4.2 5.6 - - + -
54I VAL* 3.8 29.2 - - + +
57I LEU* 3.9 20.0 - - + +
58I PRO 3.7 22.4 - - - +
59I GLU* 4.2 5.4 - - + -
79I LEU 3.7 9.9 - - - +
80I VAL* 1.3 100.7 - - + +
82I ALA* 1.3 60.0 + - - +
97I VAL* 3.8 13.0 - - + -
98I LEU 4.0 5.6 - - - +
99I CYS* 4.0 6.9 - - - -
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Residues in contact with ALA 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I VAL* 3.5 18.3 - - - +
80I VAL 4.4 4.0 - - - +
81I PRO* 1.3 75.8 - - - +
83I ALA* 1.3 59.0 + - + +
98I LEU* 2.8 19.3 + - + +
99I CYS* 4.6 0.7 - - - -
100I GLU* 4.5 8.1 - - + +
114I ARG* 3.5 47.4 + - - +
216I ASP* 4.8 0.6 - - - +
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Residues in contact with ALA 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I VAL* 4.0 4.3 - - - -
82I ALA* 1.3 79.5 - - - +
84I MET* 1.3 59.4 + - - +
85I PHE* 4.1 18.5 - - + -
96I LEU 4.2 0.3 - - - +
97I VAL* 3.6 1.6 - - - -
98I LEU* 2.8 39.3 + - + +
216I ASP* 3.4 35.0 - - + +
217I HIS* 6.1 0.2 - - + -
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Residues in contact with MET 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I PRO* 3.9 24.9 - - - +
52I LYS 4.0 2.9 - - - +
53I CYS* 3.3 39.9 - - - +
54I VAL* 3.8 22.0 - - + +
57I LEU* 3.7 25.8 - - + -
83I ALA* 1.3 74.0 - - - +
85I PHE* 1.3 80.9 + - - +
95I LYS* 4.1 19.5 - - + +
96I LEU 3.4 10.3 - - - +
97I VAL* 4.5 1.1 - - - +
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Residues in contact with PHE 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I ALA* 4.1 23.8 - - + -
84I MET* 1.3 81.3 - - - +
86I ARG* 1.3 65.8 + - - +
95I LYS* 3.4 10.6 - - - +
96I LEU* 2.8 38.5 + - + +
98I LEU 5.6 0.2 - - - -
186I ALA* 3.4 20.2 - - + +
187I GLY* 3.7 19.7 - - - -
188I VAL* 4.0 7.6 - - + -
216I ASP 4.4 1.1 - - - -
217I HIS* 3.6 43.3 - + - -
220I VAL* 3.4 42.6 - - + -
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Residues in contact with ARG 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H PRO* 5.2 4.6 + - - +
22H GLN 6.3 0.6 - - - -
85I PHE* 1.3 77.6 - - - +
87I ASP* 1.3 59.9 + - - +
88I PRO* 3.3 11.8 - - - +
92I ASP* 2.7 42.4 + - - +
94I ASN 4.0 4.7 - - - -
95I LYS* 4.5 12.8 - - - +
96I LEU* 3.9 4.4 - - - +
184I LEU 5.2 0.4 + - - -
185I TYR* 2.9 66.4 + - + +
186I ALA* 3.0 22.1 + - - +
187I GLY* 5.9 0.9 - - - -
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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