Contacts of the strand formed by residues 24 - 33 (chain K) in PDB entry 2MXU
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 VAL 24 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20J PHE* 3.8 17.7 - - + -
23J ASP* 3.1 7.9 + - - +
24J VAL* 3.3 9.3 - - + +
25J GLY 3.2 17.8 + - - -
20K PHE* 3.7 26.2 - - + -
21K ALA 3.8 13.5 - - - +
22K GLU 4.4 1.1 - - - +
23K ASP* 1.3 81.2 + - - +
25K GLY* 1.3 63.6 + - - +
26K SER 3.5 27.9 + - - +
27K ASN* 4.1 4.9 - - + +
22L GLU 6.2 0.2 - - - -
24L VAL* 3.4 15.5 - - + +
27L ASN* 4.0 19.5 - - + +
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Residues in contact with GLY 25 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25J GLY* 3.3 25.6 - - - -
26J SER 3.6 0.7 + - - -
23K ASP* 5.0 1.4 + - - -
24K VAL* 1.3 69.4 - - - +
26K SER* 1.3 61.8 + - - +
24L VAL 3.0 13.7 + - - -
25L GLY* 3.2 12.7 + - - -
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Residues in contact with SER 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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26J SER* 3.4 20.6 - - - +
24K VAL* 3.5 7.6 - - - +
25K GLY* 1.3 76.7 - - - +
27K ASN* 1.3 61.0 + - - +
25L GLY 3.6 4.6 + - - -
26L SER* 3.0 25.1 + - - -
27L ASN 2.9 26.6 + - - +
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Residues in contact with ASN 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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20J PHE* 3.3 35.4 - - + -
24J VAL* 4.2 8.8 - - + +
26J SER 3.0 7.9 + - - +
27J ASN* 2.9 26.2 + - - +
28J LYS* 2.9 26.5 + - - +
29J GLY 4.3 3.6 + - - -
30J ALA* 3.7 11.7 - - - +
24K VAL* 4.1 3.1 - - + +
26K SER* 1.3 72.8 - - - +
28K LYS* 1.3 62.0 + - - +
30K ALA* 3.3 17.5 - - - +
27L ASN* 2.9 32.7 + - - +
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Residues in contact with LYS 28 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28J LYS* 3.3 26.7 - - + +
41J ILE* 5.1 2.2 - - + +
42J ALA* 2.8 35.9 + - - -
27K ASN* 1.3 77.0 - - - +
29K GLY* 1.3 63.9 + - - +
30K ALA* 3.5 5.0 + - - +
41K ILE* 6.4 0.2 - - + -
42K ALA* 2.8 35.2 + - - +
27L ASN 2.9 16.5 + - - +
28L LYS* 3.4 21.7 - - + +
29L GLY 3.0 24.3 + - - -
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Residues in contact with GLY 29 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28J LYS 3.1 5.4 + - - -
29J GLY 3.0 18.0 + - - -
41J ILE* 4.3 12.8 - - - +
28K LYS* 1.3 73.9 - - - +
30K ALA* 1.3 57.8 + - - +
31K ILE* 4.0 6.7 - - - -
41K ILE* 3.8 20.5 - - - +
42K ALA 5.8 0.2 - - - -
29L GLY* 3.4 19.4 - - - -
31L ILE* 3.5 12.8 - - - +
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Residues in contact with ALA 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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20J PHE* 4.9 1.1 - - + -
29J GLY 3.2 4.9 + - - -
30J ALA* 3.4 4.7 - - - -
31J ILE 3.3 13.0 + - - -
19K PHE* 3.3 26.7 - - + -
20K PHE* 4.9 1.1 - - + -
27K ASN* 3.3 31.4 - - - +
28K LYS 3.5 0.4 - - - +
29K GLY* 1.3 71.3 - - - +
31K ILE* 1.3 67.5 + - - +
27L ASN* 3.5 15.7 - - - +
30L ALA 3.5 8.5 - - - +
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Residues in contact with ILE 31 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29J GLY 4.3 1.1 - - - +
31J ILE* 3.4 38.6 - - + +
35J MET* 3.8 21.5 - - + -
41J ILE* 3.6 17.3 - - + -
19K PHE* 3.2 12.9 - - - -
29K GLY 3.8 4.3 - - - +
30K ALA* 1.3 94.9 - - - +
32K ILE* 1.3 61.4 + - - +
35K MET* 3.4 24.9 - - + -
39K VAL* 5.2 3.1 - - + -
41K ILE* 4.0 10.1 - - + -
30L ALA 3.2 7.7 + - - -
31L ILE* 3.4 26.0 - - + +
32L ILE 3.1 23.0 + - - -
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Residues in contact with ILE 32 (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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19J PHE* 4.0 1.1 - - + -
31J ILE 3.2 3.7 + - - +
32J ILE* 3.3 35.0 - - + +
33J GLY 3.3 20.4 + - - -
35J MET* 4.5 0.5 - - - +
17K LEU* 3.8 27.6 - - + -
18K VAL 5.4 0.7 - - - +
19K PHE* 3.3 33.7 - - + +
31K ILE* 1.3 78.6 - - - +
33K GLY* 1.3 62.6 + - - +
35K MET* 4.9 0.2 - - - -
17L LEU* 4.0 20.4 - - + -
19L PHE* 5.7 0.7 - - + -
32L ILE* 3.3 28.5 - - + +
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Residues in contact with GLY 33 (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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32J ILE* 5.9 0.2 - - - -
33J GLY 3.0 14.4 - - - -
35J MET* 4.9 0.7 - - - -
32K ILE* 1.3 78.7 - - - +
34K LEU* 1.3 63.5 + - - -
35K MET* 3.5 14.9 - - - +
32L ILE 3.2 6.5 + - - -
33L GLY* 3.0 26.2 - - - -
34L LEU 3.5 0.2 + - - -
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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