Contacts of the strand formed by residues 70 - 78 (chain B) in PDB entry 4QKB
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 ILE 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B ASP* 5.7 0.3 - - - -
65B HIS 5.6 0.9 + - - -
68B ALA* 3.5 11.0 - - - +
69B ALA* 1.3 84.2 - - + +
71B HIS* 1.3 68.4 + - - +
73B PHE* 3.3 41.5 - - + -
75B GLU* 4.5 11.0 - - - +
108B HIS* 4.8 0.7 - - + -
110B LEU* 3.9 20.2 - - + -
112B LEU* 3.6 28.0 - - + -
117B TYR 3.7 2.0 - - - -
118B ILE* 3.9 19.1 - - + -
121B HIS* 5.8 0.2 - - + -
302B AKG 3.7 25.6 - - - +
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Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLU* 5.8 0.7 - - + -
106A SER* 5.5 6.5 - - - -
64B ASP* 3.6 22.5 - - + +
65B HIS 2.9 30.8 + - - -
66B TRP* 4.2 5.8 - - - -
68B ALA 2.7 29.1 + - - -
69B ALA 3.5 7.0 - - - -
70B ILE* 1.3 75.2 - - - +
72B GLY* 1.3 65.2 + - - +
73B PHE* 3.7 2.5 - - - -
112B LEU* 3.7 3.3 - - - +
116B GLY* 3.2 2.0 - - - -
117B TYR* 2.9 70.4 + + + +
119B LYS* 3.7 16.4 + - + -
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B TYR* 4.2 1.1 - - - -
62B GLU 5.3 1.1 - - - -
64B ASP* 2.8 22.8 + - - -
71B HIS* 1.3 75.0 - - - +
73B PHE* 1.3 60.0 + - - +
112B LEU* 3.5 3.3 - - - -
113B GLU* 3.1 55.4 + - - +
115B ARG 5.5 0.2 - - - -
116B GLY* 3.9 4.7 - - - -
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B TYR* 3.4 9.9 - - - +
62B GLU* 2.7 72.0 + - + +
63B TYR 4.9 6.5 - - - -
64B ASP* 4.7 4.4 + - - -
65B HIS* 6.1 0.9 - - - -
68B ALA* 5.6 5.6 - - + -
70B ILE* 3.3 55.4 - - + -
71B HIS* 4.6 0.7 - - - -
72B GLY* 1.3 84.4 - - - +
74B ARG* 1.3 58.5 + - - +
75B GLU* 3.7 27.6 - - + -
110B LEU* 3.8 20.2 - - + -
111B ASP 3.3 12.6 - - - +
112B LEU* 4.1 2.2 - - + -
113B GLU* 4.5 0.2 + - - -
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLU* 4.8 2.4 + - - -
56B LEU* 3.3 26.6 + - + +
57B ARG* 3.8 17.2 + - - +
59B ARG* 3.0 34.8 + - + -
60B ARG 3.5 16.6 - - - +
61B TYR* 3.2 39.1 + - + -
62B GLU* 4.4 6.3 - - + -
73B PHE* 1.3 75.9 - - - +
75B GLU* 1.3 64.0 + - - +
110B LEU* 4.0 2.1 - - - +
111B ASP* 2.7 57.5 + - + +
196B ARG* 3.6 16.2 - - - +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 4.4 4.5 - - - -
59B ARG* 2.8 27.5 + - - -
62B GLU* 3.9 3.5 + - - +
70B ILE* 4.5 4.3 - - - +
73B PHE* 3.7 19.8 - - + -
74B ARG* 1.3 78.7 - - - +
76B THR* 1.3 64.5 + - - +
108B HIS* 2.9 31.6 + - + +
109B VAL 3.2 13.2 - - - +
110B LEU* 4.3 6.0 - - + +
303B MN 2.4 35.3 + - - +
64C ASP 6.1 0.2 - - - -
65C HIS* 3.0 17.7 - - - -
66C TRP* 5.8 0.7 - - - -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU* 5.3 2.9 - - + -
55B GLU* 4.5 23.3 + - + +
56B LEU* 3.8 17.5 - - + +
59B ARG* 3.8 27.5 + - - +
75B GLU* 1.3 77.3 - - - +
77B GLU* 1.3 73.5 + - - +
78B LYS* 4.9 1.3 - - + -
108B HIS* 3.7 4.3 - - - -
109B VAL* 2.7 57.4 + - + +
64C ASP 5.1 2.0 - - - -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ARG* 5.2 1.4 - - - +
76B THR* 1.3 79.3 + - - +
78B LYS* 1.3 59.8 + - - +
79B SER* 4.4 1.0 + - - -
106B SER* 2.6 37.5 + - - +
107B VAL 3.5 6.9 - - - +
108B HIS* 3.3 33.3 + - - +
64C ASP* 3.2 41.9 + - + +
65C HIS* 4.3 1.7 - - - -
66C TRP* 3.4 35.4 + - - +
71C HIS* 5.5 1.8 - - + -
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU* 3.1 25.3 + - - +
52B LEU* 3.6 23.6 - - + -
55B GLU* 2.9 36.5 + - - +
76B THR* 4.0 3.1 - - + +
77B GLU* 1.3 73.7 - - - +
79B SER* 1.3 63.2 + - - +
80B ARG 3.0 26.4 + - - +
81B TRP* 3.3 41.7 + - + -
106B SER* 3.4 1.8 - - - -
107B VAL* 2.7 44.1 + - - +
109B VAL* 4.5 8.1 - - + -
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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