Contacts of the strand formed by residues 61 - 66 (chain D) in PDB entry 4YHP
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 PHE 61 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D GLN* 4.3 11.0 - - - -
46D VAL* 4.3 20.0 - - + +
47D VAL* 4.3 13.7 - - + +
53D ARG* 2.4 36.2 + - - -
57D ILE* 4.0 20.2 - - + -
58D PRO* 3.5 37.0 - - + +
59D GLU 3.0 1.7 - - - +
60D ARG* 1.3 90.9 - - - +
62D SER* 1.3 53.2 + - - +
72D LEU* 4.6 4.0 - - + -
73D THR 3.4 2.5 - - - -
74D ILE* 3.6 39.3 - - + -
81D ASP* 3.6 20.9 - - - -
85D TYR* 3.9 13.9 - + - -
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Residues in contact with SER 62 (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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47D VAL* 3.9 9.2 - - - +
51D SER 5.5 2.0 - - - -
53D ARG* 3.9 10.5 - - - +
59D GLU 4.8 3.4 - - - -
60D ARG 4.9 1.1 + - - -
61D PHE* 1.3 76.3 - - - +
63D GLY* 1.3 61.9 + - - +
72D LEU* 3.5 4.5 - - - +
73D THR* 2.9 48.2 + - - +
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Residues in contact with GLY 63 (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* 5.2 1.6 - - - -
47D VAL* 4.1 12.9 - - - +
50D ASP 3.4 17.7 - - - -
51D SER* 3.2 22.4 + - - +
62D SER* 1.3 78.5 - - - +
64D SER* 1.3 63.8 + - - -
71D THR 3.3 8.7 - - - -
72D LEU* 4.8 0.9 - - - -
73D THR* 5.9 0.2 - - - -
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Residues in contact with SER 64 (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* 5.3 0.7 + - - -
50D ASP 3.6 6.1 + - - +
51D SER* 4.8 2.7 - - - -
63D GLY* 1.3 75.2 - - - -
65D ASN* 1.3 63.7 + - - +
66D SER* 6.3 0.2 - - - -
69D THR 4.9 0.2 - - - -
70D ALA* 3.2 3.5 - - - +
71D THR* 2.8 47.9 + - - +
73D THR* 5.6 0.5 + - - -
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Residues in contact with ASN 65 (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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27D ILE* 2.6 37.7 + - - +
28D GLY* 3.5 12.4 - - - +
30D ILE 2.8 18.6 + - - -
32D VAL* 3.5 5.8 - - - +
50D ASP* 2.9 35.8 + - + +
64D SER* 1.3 77.8 - - - +
66D SER* 1.3 71.5 + - - +
69D THR 3.5 10.0 - - - +
70D ALA* 3.5 11.7 - - + +
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Residues in contact with SER 66 (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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28D GLY* 4.2 6.3 - - - -
64D SER* 6.3 0.7 - - - -
65D ASN* 1.3 79.0 + - - +
67D GLY* 1.3 68.0 + - - +
68D ASN 3.0 3.3 + - - -
69D THR* 2.9 22.1 + - - +
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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