Contacts of the strand formed by residues 37 - 46 (chain A) in PDB entry 2QME
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 PHE 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A THR* 3.6 0.6 - - - +
36A VAL* 1.3 85.4 - - + +
38A ASP* 1.3 77.5 + - - +
39A ASN* 4.6 1.8 - - + -
56A TRP* 3.9 27.6 - + + -
57A ASP 3.8 9.4 - - - -
58A THR* 5.9 1.3 - - + -
67A LEU* 4.7 16.2 - - + -
68A ARG* 5.8 1.3 - - - -
70A LEU* 4.7 12.1 - - + -
71A SER* 3.2 31.0 - - - -
21I ILE* 3.9 29.6 - - + -
23I VAL* 2.9 52.6 + - + +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 3.5 19.1 + - - +
37A PHE* 1.3 83.8 + - - +
39A ASN* 1.3 58.3 + - - +
40A TYR* 3.4 28.9 + - + +
56A TRP* 3.7 1.9 - - - +
57A ASP* 2.7 42.9 + - + +
19I HIS* 2.8 18.1 + - - +
21I ILE 3.3 4.9 - - - +
22I HIS* 2.6 36.9 + - - -
23I VAL 4.7 0.3 - - - +
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Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 4.7 5.8 - - + -
38A ASP* 1.3 73.1 - - - +
40A TYR* 1.3 73.5 + - - +
41A SER* 5.6 0.3 - - - -
54A GLY* 4.1 3.0 - - - -
55A LEU 2.8 30.9 + - - +
56A TRP* 3.5 28.1 - - + +
19I HIS* 3.6 4.0 - - - -
20I THR* 2.3 50.1 + - - +
21I ILE* 3.0 35.6 + - + +
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Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A THR* 4.0 11.4 - - - +
20A LEU* 3.9 25.8 - - + -
21A ILE* 3.7 23.4 - - + +
24A THR* 5.2 1.1 - - - +
38A ASP* 3.4 19.9 + - + +
39A ASN* 1.3 85.4 + - - +
41A SER* 1.3 59.7 + - - +
54A GLY* 3.7 1.2 - - - -
55A LEU* 2.8 51.5 + - + +
57A ASP* 3.3 34.8 + - + -
17I PHE* 3.8 27.8 - + + -
18I GLU 3.3 6.7 - - - +
19I HIS* 3.6 34.0 - + - -
20I THR* 4.5 0.7 - - - -
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN* 5.6 0.7 - - - -
40A TYR* 1.3 76.7 - - - +
42A ALA* 1.3 62.9 + - - +
52A ASN* 3.0 25.1 + - - -
53A LEU 3.2 7.4 - - - -
54A GLY* 5.2 1.8 - - - -
55A LEU* 5.4 0.9 - - - -
16I ASP 3.5 3.6 + - - +
17I PHE* 3.3 5.6 - - - -
18I GLU* 2.9 37.9 + - - +
20I THR* 3.7 20.9 - - - -
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 4.0 28.5 - - + +
41A SER* 1.3 76.9 + - - +
43A ASN* 1.3 61.3 + - - +
52A ASN* 3.2 2.1 + - - -
53A LEU* 2.7 45.9 + - + +
55A LEU* 4.9 0.4 - - + +
14I PRO* 4.3 14.6 - - + -
15I SER 3.5 13.5 - - - +
16I ASP 4.0 3.1 - - - -
17I PHE* 4.6 2.5 - - - -
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Residues in contact with ASN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.5 24.7 - - - +
42A ALA* 1.3 74.1 - - - +
44A VAL* 1.3 64.1 + - - +
50A PRO* 5.6 3.1 - - + -
51A VAL 3.3 4.5 - - - +
52A ASN* 3.0 32.5 + - - +
13I LEU 4.3 0.3 - - - +
14I PRO* 3.3 4.5 - - - +
15I SER* 2.8 37.9 + - - +
16I ASP* 3.0 36.3 + - - +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.4 25.6 - - - +
43A ASN* 1.3 80.4 - - - +
45A MET* 1.3 62.3 + - - +
46A VAL* 3.8 12.0 + - + -
50A PRO* 3.4 3.3 - - - +
51A VAL* 2.8 36.7 + - + +
53A LEU* 4.0 14.6 - - + -
173A ILE* 3.8 24.5 - - + -
11I ILE* 4.4 6.1 - - + -
12I SER* 3.8 18.8 - - - +
13I LEU 4.5 0.2 - - - -
14I PRO* 3.5 16.2 - - + -
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Residues in contact with MET 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 1.3 72.3 - - - +
46A VAL* 1.3 61.6 + - - +
47A ASP 4.0 0.2 - - - -
48A GLY* 3.5 35.2 - - - +
49A LYS* 3.5 5.2 - - - +
50A PRO* 3.7 27.8 - - + -
10I GLU 3.6 1.6 - - - +
11I ILE* 3.3 4.7 - - - +
12I SER* 2.9 46.4 + - - +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 3.9 17.9 - - + -
45A MET* 1.3 76.0 - - - +
47A ASP* 1.3 74.3 + - + +
49A LYS* 2.7 28.3 + - - +
51A VAL* 3.6 25.4 - - + -
173A ILE* 3.9 22.4 - - + -
174A ARG* 3.9 23.3 - - - +
177A LEU* 4.8 9.2 - - + -
178A GLY 5.5 0.9 - - - +
10I GLU 3.7 2.2 - - - -
11I ILE* 4.1 14.4 - - + -
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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