Contacts of the strand formed by residues 21 - 30 (chain K) in PDB entry 3MGO
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 21 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11K SER* 3.8 6.7 + - - -
12K ARG 3.4 4.5 + - - -
13K HIS* 2.9 60.2 + - - +
14K PRO 3.7 10.7 + - - -
15K ALA* 4.1 5.7 - - - +
16K GLU 4.9 1.2 - - - +
19K LYS 4.0 5.3 + - - +
20K SER* 1.3 78.1 + - - +
22K PHE* 1.3 84.5 + - - +
69K GLU* 3.6 8.9 - - - +
70K PHE* 2.7 47.7 + - + +
72K PRO* 4.1 4.6 - - + +
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Residues in contact with PHE 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K SER* 3.1 7.8 - - - -
12K ARG* 2.9 82.9 + - + +
13K HIS* 5.6 2.0 - + - -
21K ASN* 1.3 87.5 + - - +
23K LEU* 1.3 59.8 + - - +
24K ASN* 3.6 7.4 + - - +
50K GLU* 5.6 1.3 - - - -
67K TYR* 4.1 22.9 - + - -
68K THR* 3.4 18.6 - - - -
69K GLU* 3.9 39.9 - - + -
70K PHE* 3.4 4.0 - - - -
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Residues in contact with LEU 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K VAL* 4.1 20.4 - - + -
10K TYR 3.8 7.9 - - - +
22K PHE* 1.3 71.3 - - - +
24K ASN* 1.3 63.3 + - - +
39K LEU* 3.7 31.4 - - + +
40K LEU 4.8 1.3 - - - +
46K ILE* 4.8 1.3 - - + -
67K TYR* 3.2 5.9 - - - +
68K THR* 2.9 42.1 + - + +
70K PHE* 3.2 24.2 - - + -
78K TYR* 3.7 34.8 - - + -
79K ALA 5.0 4.3 - - - +
95K TRP* 4.1 23.1 - - + -
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Residues in contact with ASN 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236J ALA 3.0 29.1 + - - +
237J GLY* 5.1 1.4 - - - -
8K GLN 3.7 0.4 - - - +
9K VAL* 3.3 9.7 - - - +
10K TYR* 2.6 69.9 + - + +
12K ARG* 3.9 17.9 + - - +
22K PHE* 4.4 4.8 - - - +
23K LEU* 1.3 76.3 - - - +
25K CYS* 1.3 60.4 + - - +
26K TYR 4.1 0.4 - - - -
39K LEU* 5.3 0.4 - - - -
65K LEU* 3.9 16.1 - - + +
66K TYR 3.4 1.3 - - - -
67K TYR* 3.1 24.8 - - - +
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Residues in contact with CYS 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ILE* 4.0 16.2 - - - -
8K GLN 3.3 4.0 - - - -
9K VAL* 4.9 1.1 - - + -
23K LEU 4.2 0.2 + - - -
24K ASN* 1.3 72.8 - - - +
26K TYR* 1.3 60.9 + - - +
27K VAL* 3.8 7.0 + - - -
37K VAL* 3.9 9.9 - - + -
39K LEU* 3.7 18.3 - - + +
64K LEU 3.8 2.1 - - - +
65K LEU* 4.2 1.8 - - - -
66K TYR* 2.8 39.7 + - + +
80K CYS* 2.0 50.5 - - + -
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Residues in contact with TYR 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232J GLU* 4.0 14.1 + - + -
233J THR 4.2 11.5 + - - -
234J ARG* 4.2 8.3 - - + -
235J PRO* 3.7 38.5 - - + +
6K LYS 3.4 4.7 - - - +
7K ILE* 3.5 1.4 - - - -
8K GLN* 2.8 42.1 + - + +
10K TYR* 3.4 24.2 - - + +
25K CYS* 1.3 71.4 - - - +
27K VAL* 1.3 61.5 + - - +
28K SER* 3.8 24.6 - - - -
63K TYR* 3.5 39.4 - + + +
64K LEU 3.5 17.7 - - - -
65K LEU* 4.2 8.3 - - + -
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Residues in contact with VAL 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K PRO* 4.6 1.8 - - + -
6K LYS 3.2 7.9 - - - +
7K ILE* 4.5 4.3 - - + -
25K CYS* 3.8 11.0 + - - +
26K TYR* 1.3 76.4 - - - +
28K SER* 1.3 61.1 + - - +
30K PHE* 3.6 17.3 - - + -
35K ILE* 4.2 13.0 - - + -
37K VAL* 3.9 17.3 - - + -
63K TYR* 3.1 2.8 - - - +
64K LEU* 2.7 65.1 + - + +
66K TYR* 4.7 2.2 - - + -
82K VAL* 3.8 28.9 - - + -
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Residues in contact with SER 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232J GLU* 2.6 32.3 + - - -
5K PRO* 3.4 1.6 - - - +
6K LYS* 2.7 45.3 + - - +
26K TYR* 3.8 15.0 + - - -
27K VAL* 1.3 76.7 - - - +
29K GLY* 1.3 62.5 + - - +
30K PHE* 3.2 6.2 + - - -
57K SER* 6.0 1.1 - - - -
62K PHE 3.4 7.4 - - - -
63K TYR* 3.6 16.2 - - - -
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Residues in contact with GLY 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K ARG* 3.2 22.2 - - - +
4K THR 3.4 9.9 - - - +
6K LYS* 5.3 7.4 - - - -
28K SER* 1.3 75.5 - - - +
30K PHE* 1.3 57.7 + - - +
57K SER* 5.9 0.8 + - - -
61K SER* 3.3 25.1 + - - -
62K PHE 3.0 7.3 + - - -
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Residues in contact with PHE 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K ARG 3.1 12.3 - - - +
5K PRO* 3.6 31.9 - - + -
27K VAL* 3.6 27.1 - - + -
28K SER 3.2 9.6 - - - -
29K GLY* 1.3 80.2 - - - +
31K HIS* 1.3 65.4 + - - +
32K PRO 3.2 14.6 - - - -
33K SER* 3.7 22.2 - - - -
35K ILE* 4.0 12.3 - - + -
54K LEU* 4.8 0.2 - - + -
61K SER* 3.7 0.7 - - - -
62K PHE* 3.0 62.5 + - + -
63K TYR* 3.9 0.9 - - - -
64K LEU* 4.0 23.3 - - + -
84K HIS* 4.0 7.2 - + - +
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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