Contacts of the strand formed by residues 66 - 71 (chain D) in PDB entry 1MWA
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 LYS 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D HIS* 3.6 6.7 - - - -
65D TYR* 1.3 80.6 - - - +
67D ALA* 1.3 66.3 + - - +
68D SER* 6.2 0.4 - - - -
77D LEU* 3.1 7.7 - - - +
78D ILE* 2.5 65.8 + - + +
79D LEU* 5.4 1.1 - - - -
80D GLU* 5.4 8.3 + - - +
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Residues in contact with ALA 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TRP* 4.9 2.5 - - + -
47D HIS* 3.4 36.8 - - + +
55D THR* 3.9 18.5 + - + +
66D LYS* 1.3 85.0 - - - +
68D SER* 1.3 68.1 + - - +
75D PHE* 4.8 10.8 - - + -
76D SER 3.9 5.2 - - - +
77D LEU* 3.9 9.9 - - + +
78D ILE* 3.5 6.0 - - - +
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Residues in contact with SER 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D THR* 5.3 0.2 - - - +
55D THR* 4.0 5.8 + - - -
66D LYS* 6.2 0.4 - - - -
67D ALA* 1.3 81.6 - - - +
69D ARG* 1.3 52.5 + - - +
70D PRO* 2.8 31.1 - - - +
75D PHE* 3.8 5.6 - - - -
76D SER* 2.6 38.9 + - - -
78D ILE* 2.9 16.3 - - - +
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Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D HIS 4.1 8.5 + - - -
30D ASN 3.1 27.5 + - - -
32D MET* 4.1 14.9 - - - +
49D SER* 2.4 25.4 + - - -
51D GLY* 2.6 22.8 + - - -
53D GLY* 3.2 31.1 - - - +
54D SER 3.1 27.1 - - - +
55D THR* 3.9 3.4 + - - -
68D SER* 1.3 71.1 - - - +
70D PRO* 1.3 58.3 - - - +
71D SER 2.6 39.5 + - - +
72D GLN* 3.4 12.1 - - - +
74D ASN 3.1 10.1 + - - -
75D PHE* 3.1 27.6 - - - -
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Residues in contact with PRO 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D SER* 2.8 32.1 - - - +
69D ARG* 1.3 74.0 - - - +
71D SER* 1.3 70.7 + - - +
74D ASN* 4.1 13.9 - - + +
75D PHE* 4.0 16.8 - - - +
76D SER* 4.3 8.5 - - - +
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Residues in contact with SER 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ALA* 4.7 3.6 - - - +
53D GLY 4.9 4.9 - - - +
69D ARG* 2.6 32.1 + - - +
70D PRO* 1.3 84.3 + - - +
72D GLN* 1.3 55.6 + - - +
73D GLU* 3.0 17.3 + - - +
74D ASN* 2.9 31.9 + - - +
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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