Contacts of the strand formed by residues 19 - 26 (chain A) in PDB entry 4MD4
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 SER 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 4.0 10.7 - - - -
13A TYR* 3.4 3.7 - - - -
14A LEU* 2.8 52.3 + - - +
17A ASP* 3.9 14.8 - - - +
18A GLN* 1.3 78.2 - - - +
20A GLY* 1.3 59.4 + - - +
21A GLU* 6.1 0.9 - - - -
115A PRO 5.2 1.6 + - - -
116A VAL* 5.2 2.8 - - - +
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Residues in contact with GLY 20 (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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12A PHE* 3.2 13.0 - - - -
13A TYR* 4.1 8.8 - - - -
18A GLN 4.1 1.4 + - - -
19A SER* 1.3 75.1 - - - +
21A GLU* 1.3 71.1 + - - +
36A MET* 3.5 21.2 - - - +
63A ILE* 4.0 14.6 - - - -
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Residues in contact with GLU 21 (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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10A ALA 4.6 0.7 - - - -
11A GLU* 3.2 6.2 - - - -
12A PHE* 3.1 64.0 + - + -
19A SER* 5.7 1.1 - - - -
20A GLY* 1.3 80.2 - - - +
22A PHE* 1.3 62.5 + - - +
23A MET* 5.9 3.8 - - + +
33A HIS* 6.4 1.1 - - + -
34A VAL 5.4 1.8 - - - +
36A MET* 3.7 7.2 - - - -
63A ILE* 3.5 7.4 - - - +
136A VAL* 3.4 24.7 - - + +
137A PHE* 3.2 40.8 + - - +
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Residues in contact with PHE 22 (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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9A GLN* 3.4 39.0 - - + -
10A ALA 3.7 4.3 - - - -
11A GLU* 3.7 20.2 - - + +
21A GLU* 1.3 77.4 - - - +
23A MET* 1.3 63.8 + - - +
24A PHE* 3.8 20.0 - + - -
32A PHE* 4.3 2.9 - + - -
33A HIS* 3.2 5.6 - - - +
34A VAL* 3.0 33.1 + - + -
36A MET* 3.4 20.5 - - + +
54A PHE* 3.6 32.5 - + - -
59A ALA* 3.4 31.4 - - + -
62A ASN* 4.1 2.9 - - + -
63A ILE* 4.8 2.5 - - + -
6C VAL* 3.9 9.9 - - + -
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Residues in contact with MET 23 (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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9A GLN* 3.3 5.4 - - - +
10A ALA* 2.8 50.0 + - + +
21A GLU* 5.9 2.9 - - + +
22A PHE* 1.3 79.5 - - - +
24A PHE* 1.3 84.3 + - - +
25A ASP* 3.9 17.0 - - + +
30A GLU* 3.8 14.1 - - + -
32A PHE* 3.3 13.9 - - - +
33A HIS* 3.8 10.8 - - + +
136A VAL* 5.0 3.6 - - + -
137A PHE 4.7 8.3 - - - +
138A LEU* 3.8 22.0 - - + -
139A PRO* 3.7 32.1 - - + -
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Residues in contact with PHE 24 (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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7A ILE* 3.9 24.9 - - + -
8A ILE 3.3 6.1 - - - -
9A GLN* 3.5 34.8 - - + -
22A PHE* 3.8 12.3 - + - -
23A MET* 1.3 81.1 - - - +
25A ASP* 1.3 57.2 + - - +
30A GLU* 3.5 4.3 - - - -
31A ILE* 2.8 39.0 + - + -
32A PHE* 3.0 50.0 + + + +
54A PHE* 4.7 3.8 - + - -
78B TYR* 3.9 9.0 - - - -
82B ASN* 3.7 18.2 - - - -
4C TYR* 4.2 17.3 - + + -
5C CIR 3.9 16.2 - - - -
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Residues in contact with ASP 25 (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 VAL 3.7 1.4 - - - +
7A ILE* 3.2 8.7 - - - +
8A ILE* 2.8 49.5 + - + +
23A MET* 3.9 16.9 - - + +
24A PHE* 1.3 75.0 - - - +
26A PHE* 1.3 60.3 + - - +
27A ASP* 3.6 2.3 + - - -
28A GLY* 2.7 44.9 + - - -
29A ASP 3.2 8.8 + - - +
31A ILE* 4.4 2.0 - - - -
139A PRO* 4.1 13.3 - - + +
146A ARG* 3.5 13.0 + - - -
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Residues in contact with PHE 26 (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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5A HIS* 3.4 36.3 - + + -
6A VAL 3.6 2.9 - - - -
7A ILE* 3.8 25.6 - - + -
25A ASP* 1.3 72.7 - - - +
27A ASP* 1.3 78.7 + - - +
28A GLY 3.1 0.2 - - - -
29A ASP* 2.7 24.8 + - - +
31A ILE* 3.9 14.3 - - + +
83B TYR* 5.4 0.4 - + - -
90B THR* 3.7 29.6 - - + -
91B VAL* 3.6 27.8 - - + -
123B TYR* 3.4 24.9 + + - -
153B TRP* 3.7 21.3 - + + -
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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