Contacts of the strand formed by residues 119 - 125 (chain A) in PDB entry 3EDY
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A THR* 3.9 18.6 - - + -
51A PHE 3.6 2.9 - - - -
52A ALA* 3.9 20.9 - - + -
53A LEU* 4.6 2.0 - - - -
112A HIS 4.7 0.4 - - - -
113A SER* 2.9 30.2 + - - -
114A VAL* 3.8 10.2 + - + +
117A GLN 4.4 0.3 - - - -
118A ASP* 1.3 91.1 + - - +
120A LEU* 1.3 61.3 + - - +
305A LEU* 4.1 25.1 - - + -
309A MET* 3.7 50.0 - - + -
312A SER* 5.4 0.4 - - - -
339A ARG* 3.3 28.7 - - + -
343A GLU* 3.4 32.5 - - + -
346A LYS* 4.6 0.7 - - - -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE* 2.9 44.6 + - + +
53A LEU* 4.2 19.3 - - + -
96A LEU* 6.5 0.2 - - + -
99A VAL* 4.7 7.2 - - + -
100A GLN* 4.5 23.6 - - + +
103A LEU* 3.9 22.4 - - + -
111A CYS* 4.1 14.1 - - + -
112A HIS 3.2 24.9 - - - +
113A SER* 4.0 12.8 - - - +
119A PHE* 1.3 74.4 - - - +
121A THR* 1.3 61.3 + - - +
122A CYS* 4.2 9.9 - - - -
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A SER* 2.9 29.6 - - - +
49A LEU 3.4 11.9 - - - +
50A THR* 2.9 28.4 + - - +
110A LYS 4.1 1.0 - - - +
111A CYS* 2.9 25.8 - - - +
112A HIS* 2.9 22.9 + - - +
120A LEU* 1.3 72.4 - - - +
122A CYS* 1.3 63.1 + - - +
301A GLN* 6.3 1.8 - - + +
306A GLN* 6.0 2.0 - - - +
309A MET* 3.7 16.3 - - + +
566A NAG 4.8 6.7 - - - +
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Residues in contact with CYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A SER* 3.3 3.9 - - - -
49A LEU* 3.0 30.7 + - - +
51A PHE* 4.9 8.3 - - + -
103A LEU* 4.0 21.1 - - - -
108A ALA* 3.7 21.3 - - + -
109A GLN 3.8 1.3 - - - -
110A LYS 4.4 0.7 - - - -
111A CYS* 2.1 49.4 - - - +
120A LEU* 4.2 7.4 - - - -
121A THR* 1.3 77.7 - - - +
123A TRP* 1.3 63.7 + - - +
124A LEU* 3.7 5.0 + - + +
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Residues in contact with TRP 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU* 3.7 29.9 - - + +
47A LEU* 3.3 42.6 - - - -
48A SER* 3.8 18.6 + - - -
107A GLY 4.1 1.4 - - - +
108A ALA* 3.5 5.4 - - - -
109A GLN* 2.9 42.5 + - + +
110A LYS* 3.7 38.4 + - + +
112A HIS* 5.3 7.2 - + - -
122A CYS* 1.3 71.7 - - - +
124A LEU* 1.3 60.4 + - - +
298A HIS* 6.4 2.5 - - - -
301A GLN* 6.3 0.7 - - - -
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU* 3.2 9.0 - - - -
47A LEU* 2.6 43.4 + - + +
49A LEU* 4.2 23.6 - - + -
51A PHE* 4.5 11.4 - - + -
103A LEU* 4.9 1.8 - - + +
106A ALA* 4.0 21.1 - - + +
107A GLY 4.0 4.0 - - - -
108A ALA* 3.6 35.0 - - + +
122A CYS* 3.7 4.2 + - + +
123A TRP* 1.3 74.9 - - - +
125A SER* 1.3 66.4 + - - +
128A GLN* 4.0 9.9 - - + +
129A ALA* 4.2 11.4 - - + +
132A LEU* 4.0 24.2 - - + -
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PRO 3.8 9.0 - - - -
44A GLU* 4.7 8.7 - - - -
45A GLU 3.1 10.8 - - - -
46A GLU* 3.4 17.8 + - - -
47A LEU* 4.2 1.3 - - - -
124A LEU* 1.3 75.5 - - - +
126A ILE* 1.3 58.4 + - - +
127A ARG* 3.6 6.8 + - - +
128A GLN* 3.0 42.7 + - - +
129A ALA* 2.8 27.5 + - - +
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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