Contacts of the strand formed by residues 29 - 38 (chain A) in PDB entry 4DDG
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A PRO* 3.4 13.7 - - - +
26A VAL* 3.0 14.4 + - + +
28A ASP* 1.3 77.5 - - + +
30A MET* 1.3 65.1 + - - +
31A PHE* 3.2 9.5 + - - +
32A HIS* 3.1 50.0 + - + +
55A HIS* 5.7 0.2 - - - -
29B ASP* 5.0 8.4 + - - +
26C VAL 5.5 1.6 - - - +
28C ASP* 3.9 20.6 + - - +
29C ASP* 5.2 10.6 + - - +
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Residues in contact with MET 30 (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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3A LEU* 3.8 31.2 - - + -
6A ILE* 3.6 23.8 - - + +
7A HIS* 3.7 33.0 - - + +
10A LEU* 4.7 9.0 - - + -
25A PRO* 3.7 34.1 - - + -
27A GLY 5.2 2.9 - - - +
28A ASP 3.3 11.4 + - - +
29A ASP* 1.3 75.9 + - - +
31A PHE* 1.3 64.1 + - + +
32A HIS 3.3 0.4 - - - -
33A TRP* 2.7 26.9 + - - +
56A PHE* 3.9 0.9 - - - -
28C ASP* 5.6 1.5 + - - +
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Residues in contact with PHE 31 (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 GLY 5.1 3.1 - - - -
2A ALA* 4.5 8.3 - - + -
3A LEU* 3.7 36.6 - - + -
6A ILE* 3.7 20.9 - - + -
29A ASP* 3.2 7.0 + - - +
30A MET* 1.3 82.1 - - + +
32A HIS* 1.3 57.9 + - - +
54A ILE 3.3 0.9 - - - +
55A HIS* 3.3 10.2 - - + +
56A PHE* 2.9 57.3 + - + +
57A PRO 4.0 12.1 - - - -
58A THR* 4.2 11.4 - - - -
26C VAL 5.4 0.4 - - - +
27C GLY* 4.0 3.8 - - - -
28C ASP* 3.1 56.1 - - + +
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Residues in contact with HIS 32 (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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26A VAL* 2.8 48.4 + - + +
29A ASP* 3.1 32.1 + - + +
30A MET 3.3 0.2 - - - -
31A PHE* 1.3 78.1 - - - +
33A TRP* 1.3 77.1 + - - +
34A GLN* 5.7 0.2 - - + -
53A THR* 3.9 18.9 - - + +
54A ILE 3.5 4.2 + - - -
55A HIS* 3.6 37.1 + + + -
55B HIS* 6.1 1.1 + - - -
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Residues in contact with TRP 33 (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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6A ILE* 3.7 20.8 - - + +
9A GLU* 4.6 2.9 - - + -
10A LEU* 3.6 53.6 - - + -
13A LEU* 4.2 11.7 - - + -
23A ALA* 4.0 8.3 - - + -
24A GLY 3.2 25.1 - - - +
25A PRO* 3.4 16.5 - - + +
26A VAL* 4.0 1.1 - - - -
30A MET* 2.7 30.2 + - - +
32A HIS* 1.3 88.1 + - - +
34A GLN* 1.3 61.5 + - - +
53A THR* 3.6 2.4 - - - -
54A ILE* 2.9 48.6 + - + -
56A PHE* 3.5 24.1 - + - -
99A ILE* 4.0 22.9 - - + -
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Residues in contact with GLN 34 (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 ALA* 3.3 4.6 - - - -
24A GLY 2.8 29.4 + - - +
25A PRO 6.0 0.2 - - - -
26A VAL* 3.9 16.0 - - + +
33A TRP* 1.3 75.1 - - - +
35A ALA* 1.3 66.3 + - - +
36A THR* 4.1 6.5 + - - +
51A PHE* 4.0 31.6 - - + +
52A LEU 3.4 11.2 - - - +
53A THR* 4.8 7.8 - - + +
54A ILE* 5.0 0.2 - - - -
70A THR* 5.7 0.8 + - - +
1028A GLU* 3.6 20.1 + - - +
66B LYS* 5.9 1.6 + - - -
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Residues in contact with ALA 35 (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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22A SER 3.5 6.3 - - - +
23A ALA* 3.6 16.4 - - + -
33A TRP 4.2 0.6 - - - -
34A GLN* 1.3 73.6 - - - +
36A THR* 1.3 61.5 + - - +
37A ILE* 3.9 8.3 - - + -
50A PHE 3.7 0.5 - - - +
51A PHE* 3.3 9.7 - - - -
52A LEU* 2.9 57.3 + - + +
54A ILE* 4.0 10.5 - - + +
103A LEU* 4.4 5.4 - - + -
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Residues in contact with THR 36 (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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20A GLN 3.5 3.1 - - - +
21A CYS* 3.5 2.1 - - - -
22A SER* 2.8 38.0 + - - -
34A GLN* 4.1 6.7 + - - -
35A ALA* 1.3 73.4 - - - +
37A ILE* 1.3 60.2 + - - +
38A MET* 4.6 14.5 - - + +
49A VAL* 4.0 24.5 - - + -
50A PHE 3.8 2.7 - - - -
51A PHE* 3.5 20.7 - - + -
1028A GLU* 4.7 8.1 - - + +
1029A ALA* 5.4 10.1 - - - +
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Residues in contact with ILE 37 (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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20A GLN 3.6 2.5 - - - -
21A CYS* 3.6 23.3 - - + -
22A SER 5.1 0.4 - - - +
35A ALA* 4.4 10.5 - - + -
36A THR* 1.3 78.1 - - - +
38A MET* 1.3 63.6 + - - +
49A VAL* 3.9 0.3 - - - -
50A PHE* 2.9 51.5 + - + +
52A LEU* 3.8 20.4 - - + -
69A PHE* 4.0 22.4 - - + -
103A LEU* 5.2 5.2 - - + +
106A ILE* 4.2 13.7 - - + -
107A CYS* 4.3 12.1 - - - -
110A LEU* 3.9 27.4 - - + -
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Residues in contact with MET 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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19A ALA 3.9 19.7 - - - +
20A GLN* 3.0 38.4 + - + +
36A THR* 4.6 10.5 - - + +
37A ILE* 1.3 78.6 - - - +
39A GLY* 1.3 70.1 + - - +
40A PRO* 3.1 9.0 - - - +
47A GLY 6.2 0.4 - - - -
48A GLY 3.8 8.7 - - - +
49A VAL* 3.9 27.4 - - + -
50A PHE* 4.8 0.2 - - - -
107A CYS* 5.9 0.9 - - - -
110A LEU* 5.0 0.7 - - - +
1029A ALA* 4.5 17.0 - - + +
1032A ALA* 6.4 1.8 - - + -
1036A ARG* 4.9 12.6 - - - +
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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