Contacts of the strand formed by residues 121 - 125 (chain D) in PDB entry 3EDC
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 GLY 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D LEU 3.8 2.0 + - - -
64D ILE* 3.8 3.7 - - - +
65D GLY* 2.9 25.1 + - - +
119D VAL* 3.4 5.2 + - - +
120D SER* 1.3 79.6 - - - +
122D LEU* 1.3 63.4 + - - -
143D VAL* 4.6 3.1 - - - -
144D PRO* 3.2 15.3 - - - -
304D LEU* 3.6 20.0 - - - +
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Residues in contact with LEU 122 (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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65D GLY 3.3 6.1 - - - +
111D VAL* 3.8 10.1 - - + -
114D LEU* 3.3 46.2 - - + -
115D LEU* 3.5 23.6 - - + -
119D VAL* 4.2 8.7 - - + -
121D GLY* 1.3 76.6 - - - -
123D ILE* 1.3 63.8 + - - +
124D ILE* 3.9 17.9 - - + -
140D CYS* 3.2 31.6 - - - -
143D VAL* 4.0 5.8 - - + -
144D PRO 2.7 12.0 + - - +
145D ALA* 3.3 4.6 - - - -
146D LEU 2.8 26.7 + - - -
304D LEU* 3.4 6.8 - - - +
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Residues in contact with ILE 123 (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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64D ILE* 4.0 18.6 - - + -
65D GLY 2.8 12.9 + - - +
66D VAL* 3.3 9.5 - - + +
67D ALA 3.0 26.3 + - - +
83D ILE* 3.9 25.1 - - + -
122D LEU* 1.3 77.4 - - - +
124D ILE* 1.3 62.2 + - - +
125D ASN* 3.7 1.7 + - + +
146D LEU* 3.4 9.0 - - + +
148D LEU* 3.4 39.5 - - + -
300D SER* 3.8 29.8 - - - +
301D VAL* 4.3 4.5 - - + -
304D LEU* 4.1 15.7 - - + -
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Residues in contact with ILE 124 (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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67D ALA* 3.7 12.1 - - + -
107D CYS* 3.9 26.0 - - - -
111D VAL* 3.6 28.7 - - + -
122D LEU* 3.9 25.4 - - + -
123D ILE* 1.3 75.0 - - - +
125D ASN* 1.3 57.0 + - - +
126D TYR* 3.4 11.2 + - + +
128D LEU* 4.0 18.2 - - + -
136D VAL* 4.4 2.9 - - + -
140D CYS* 5.1 0.4 - - - -
145D ALA* 4.7 4.9 - - + -
146D LEU 2.8 13.8 + - - +
147D PHE* 3.6 28.5 - - + +
148D LEU* 2.9 26.3 + - - -
149D ASP 4.1 1.4 + - - -
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Residues in contact with ASN 125 (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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66D VAL* 5.0 7.0 - - + -
67D ALA 2.8 13.7 + - - +
68D THR* 3.4 10.4 + - - +
69D SER* 3.1 26.5 + - - -
76D PRO* 3.8 24.0 + - - +
79D ILE* 3.7 41.2 - - + +
80D VAL* 5.4 0.6 - - + +
123D ILE 3.7 2.4 + - - -
124D ILE* 1.3 70.0 - - - +
126D TYR* 1.3 59.8 + - - +
148D LEU* 3.9 25.9 - - + +
149D ASP* 4.0 12.9 - - - +
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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