Contacts of the helix formed by residues 70 - 80 (chain B) in PDB entry 1QAP
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 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B PHE* 3.7 5.1 - - + -
69B GLY* 1.3 72.7 - - - +
71B ARG* 1.3 59.7 - - + +
73B VAL* 2.9 4.2 + - - +
74B GLU* 2.8 47.3 + - - +
89B TRP* 3.6 57.6 - - + +
91B VAL 4.1 2.4 + - - -
92B ASP* 2.9 41.4 + - - +
93B ASP* 3.1 20.5 + - - +
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Residues in contact with ARG 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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15B LEU* 4.8 2.8 + - - +
18B ILE* 4.7 15.4 - - - +
19B ASN* 4.0 38.0 + - - +
22B ILE* 3.5 32.4 - - + +
69B GLY 3.5 0.8 - - - -
70B LYS* 1.3 78.5 - - + +
72B TRP* 1.3 65.6 + - + +
74B GLU* 3.7 19.8 - - + +
75B GLU* 3.2 28.3 + - + +
93B ASP* 4.3 5.4 + - - +
164B TYR* 5.7 5.5 - - + +
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Residues in contact with TRP 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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18B ILE* 4.1 10.1 - - + -
22B ILE* 3.2 52.6 - - + +
25B ALA* 4.8 5.0 - - + +
26B VAL* 3.5 15.0 - - + +
69B GLY* 2.8 24.3 + - - +
71B ARG* 1.3 82.2 - - + +
73B VAL* 1.3 62.6 + - - +
75B GLU 3.2 1.6 + - - -
76B VAL* 3.2 20.4 + - - +
93B ASP* 5.0 0.7 - - - -
123B PHE* 3.6 46.4 - + + -
127B LEU* 3.9 17.0 - - + -
161B ALA* 3.9 29.8 - - + +
164B TYR* 3.4 53.4 - + + -
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Residues in contact with VAL 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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69B GLY 2.9 14.8 + - - +
70B LYS 2.9 3.3 + - - +
72B TRP* 1.3 72.3 - - + +
74B GLU* 1.3 58.6 + - - +
75B GLU 2.9 4.3 - - - -
76B VAL* 2.9 27.8 + - - +
77B PHE* 3.4 23.6 + - + -
87B LEU* 4.8 2.2 - - + -
89B TRP* 3.7 19.1 - - + -
104B PHE* 3.5 32.8 - - + -
120B ALA* 4.2 18.8 - - + +
123B PHE* 5.9 0.2 - - + -
124B VAL* 3.5 28.7 - - + -
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Residues in contact with GLU 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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70B LYS* 2.8 31.9 + - - +
71B ARG* 3.7 24.6 - - + +
73B VAL* 1.3 76.7 - - - +
75B GLU* 1.3 57.9 + - + +
77B PHE* 4.8 1.1 - - - +
78B ILE* 2.9 40.1 + - + +
87B LEU* 4.2 28.6 - - + +
89B TRP* 4.6 8.6 + - + -
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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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22B ILE* 3.8 11.2 - - + -
23B PRO* 3.4 35.6 - - + +
26B VAL* 3.6 13.2 - - + +
71B ARG* 3.2 21.9 + - + +
72B TRP 3.2 5.3 + - - +
73B VAL 2.9 0.8 - - - -
74B GLU* 1.3 80.9 - - + +
76B VAL* 1.3 64.3 + - - +
77B PHE 3.4 0.2 - - - -
78B ILE* 4.0 15.5 - - + +
79B GLN* 2.9 53.2 + - - +
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Residues in contact with VAL 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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26B VAL* 3.7 20.6 - - + +
30B LEU* 3.7 10.4 - - + +
72B TRP 3.2 17.0 + - - +
73B VAL 2.9 7.0 + - - +
75B GLU* 1.3 78.7 - - - +
77B PHE* 1.3 62.5 - - + +
79B GLN* 3.1 4.5 + - - +
80B LEU* 3.1 44.3 + - + +
116B GLY* 3.9 21.8 - - - +
119B THR* 4.1 12.6 - - + -
120B ALA* 3.8 29.4 - - + +
123B PHE* 4.6 3.8 - - + -
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Residues in contact with PHE 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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73B VAL* 3.4 18.8 + - + +
74B GLU 4.9 1.6 - - - +
76B VAL* 1.3 82.7 - - + +
78B ILE* 1.3 65.0 + - - +
80B LEU* 3.8 4.3 - - + +
81B ALA* 2.9 28.0 + - - +
85B VAL* 4.4 21.6 - - + +
87B LEU* 4.1 22.9 - - + -
104B PHE* 5.5 0.4 - + - -
106B LEU* 3.8 31.0 - - + -
112B VAL* 4.0 28.3 - - + -
113B LEU* 4.1 13.5 - - + -
116B GLY* 3.5 37.5 - - - -
117B GLU* 4.1 3.4 - - - -
120B ALA* 4.3 15.0 - - + -
293B MET* 4.9 0.2 - - + -
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Residues in contact with ILE 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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74B GLU* 2.9 36.7 + - + +
75B GLU* 4.0 18.4 - - + +
76B VAL 3.4 0.6 - - - -
77B PHE* 1.3 75.6 - - - +
79B GLN* 1.3 65.9 + - - +
81B ALA 4.2 1.1 - - - -
82B GLY* 2.7 43.5 + - - -
83B ASP 4.8 4.7 - - - +
87B LEU* 6.2 2.0 - - + -
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Residues in contact with GLN 79 (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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23B PRO* 3.8 7.2 + - - +
26B VAL* 3.5 11.8 - - - +
27B ALA* 3.2 32.1 - - - +
30B LEU* 3.8 5.8 - - + -
38B VAL* 3.7 34.5 - - + +
75B GLU* 2.9 36.3 + - - +
76B VAL 3.1 6.7 + - - +
78B ILE* 1.3 83.7 - - - +
80B LEU* 1.3 56.1 + - - +
82B GLY 5.1 0.2 - - - -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.0 12.6 - - + -
34B LEU* 4.0 22.9 - - + -
38B VAL* 4.0 15.3 - - + -
40B ALA* 4.0 35.1 + - + +
76B VAL* 3.1 26.6 + - + +
77B PHE* 3.2 10.5 + - + +
78B ILE 3.1 0.2 - - - -
79B GLN* 1.3 77.7 - - - +
81B ALA* 1.3 62.4 + - - +
82B GLY 4.1 0.4 - - - -
112B VAL* 4.4 15.9 - - + +
115B THR* 4.8 6.5 - - - +
116B GLY* 3.6 34.3 - - - +
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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