Contacts of the strand formed by residues 27 - 36 (chain B) in PDB entry 1QQJ
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 ASN 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B THR* 3.0 18.8 + - - +
25B GLN 3.3 0.4 - - - -
26B SER* 1.3 86.1 + - - +
28B PRO* 1.3 66.1 - - - +
29B LYS* 3.1 26.9 - - - +
31B ARG* 2.9 55.8 + - - +
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Residues in contact with PRO 28 (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 SER* 3.8 11.3 + - - +
24B THR 4.2 5.4 - - - +
25B GLN 5.1 2.7 - - - +
26B SER 4.3 3.1 - - - +
27B ASN* 1.3 89.1 - - - +
29B LYS* 1.3 62.9 + - + +
30B PRO* 3.3 9.2 - - - +
116B HIS* 5.2 1.6 - - - -
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Residues in contact with LYS 29 (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 PHE 3.6 0.7 - - - +
23B SER* 4.2 1.1 - - - -
27B ASN* 3.1 17.9 - - - +
28B PRO* 1.3 76.7 - - - +
30B PRO* 1.3 92.8 + - + +
31B ARG* 2.8 47.8 + - + +
44B SER* 5.5 3.0 + - - -
63B ASP* 3.0 32.1 + - - +
64B GLU 3.9 3.6 + - - -
65B THR* 4.1 11.9 - - + -
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Residues in contact with PRO 30 (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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21B VAL* 3.7 20.4 - - + -
22B PHE 3.4 9.6 - - - +
23B SER* 4.4 1.3 - - - -
28B PRO 3.3 8.4 - - - +
29B LYS* 1.3 105.9 + - + +
31B ARG* 1.3 58.5 + - - +
65B THR* 3.5 29.8 - - + +
116B HIS* 4.1 24.7 - - + +
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Residues in contact with ARG 31 (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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21B VAL* 3.2 6.6 - - - +
22B PHE* 2.9 59.3 + - + +
23B SER* 3.6 6.7 - - - +
24B THR* 2.9 36.0 + - - +
26B SER* 4.6 1.2 + - - -
27B ASN* 2.9 44.1 + - - +
29B LYS* 2.8 48.7 + - - +
30B PRO* 1.3 75.1 - - - +
32B ILE* 1.3 62.6 + - - +
42B ASP* 3.1 26.8 + - - +
44B SER* 4.4 12.8 - - - +
62B PHE 5.8 0.2 - - - +
64B GLU 4.2 3.6 - - - -
108B THR* 5.1 3.4 + - - -
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Residues in contact with ILE 32 (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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19B TYR* 4.9 1.1 - - + -
20B GLY 3.3 7.2 - - - +
21B VAL* 4.4 7.4 - - + -
22B PHE* 4.0 1.7 - - - -
31B ARG* 1.3 74.7 - - - +
33B GLY* 1.3 64.5 + - - +
42B ASP* 3.7 6.6 - - - +
43B LEU* 2.9 49.2 + - + +
44B SER 4.1 0.7 + - - +
61B VAL 3.3 27.1 - - - +
62B PHE* 4.0 21.1 + - + +
64B GLU 3.5 21.2 + - - +
66B THR 3.6 16.6 - - - +
67B LEU* 3.7 32.8 - - + -
70B PHE* 5.5 1.8 - - + -
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Residues in contact with GLY 33 (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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19B TYR* 3.5 5.0 - - - -
20B GLY 2.8 32.8 + - - -
22B PHE* 3.8 4.2 - - - -
31B ARG 3.7 2.2 + - - -
32B ILE* 1.3 76.9 - - - +
34B VAL* 1.3 64.8 + - - +
40B ILE* 3.7 14.8 - - - -
41B LEU 3.1 11.9 - - - -
43B LEU* 4.4 1.6 - - - -
262B TRP* 4.0 5.2 - - - -
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Residues in contact with VAL 34 (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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17B LEU* 3.8 30.3 - - + -
18B PRO 3.2 10.5 - - - +
19B TYR* 3.5 38.1 - - + -
33B GLY* 1.3 75.1 - - - -
35B ALA* 1.3 74.8 + - - +
36B ILE* 3.7 1.2 + - - +
40B ILE* 3.4 1.0 - - - -
41B LEU* 2.8 39.4 + - + +
43B LEU* 3.9 13.2 - - + -
85B LEU* 3.9 16.6 - - + -
89B LEU* 5.0 5.8 - - + -
262B TRP* 4.0 2.5 - - - -
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Residues in contact with ALA 35 (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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12B PHE* 3.7 34.7 - - + +
17B LEU* 3.9 6.1 + - - +
18B PRO* 3.3 28.9 + - + +
34B VAL* 1.3 76.9 - - - +
36B ILE* 1.3 62.0 + - - +
39B GLN 3.6 5.8 - - - -
110B GLN* 3.8 11.0 - - - +
262B TRP* 3.5 24.6 - - + -
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Residues in contact with ILE 36 (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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2B SER* 4.1 14.6 - - - +
4B ILE* 3.8 22.7 - - + +
6B VAL* 4.0 9.0 - - + -
12B PHE 3.5 16.2 - - - +
13B PRO 3.8 2.5 - - - +
14B ILE* 3.7 28.7 - - + +
17B LEU* 4.2 6.3 - - + -
34B VAL 4.3 7.0 - - - +
35B ALA* 1.3 75.9 - - - +
37B GLY* 1.3 67.8 + - - +
38B ASP 3.2 0.2 + - - -
39B GLN* 2.9 29.4 + - + +
41B LEU* 4.6 2.0 - - + +
89B LEU* 4.3 19.7 - - + -
107B PHE* 4.0 27.1 - - + -
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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