Contacts of the strand formed by residues 7 - 13 (chain A) in PDB entry 3ASZ
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 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A PRO* 1.3 70.1 - - - +
8A VAL* 1.3 58.8 + - - +
9A ILE* 3.4 31.9 - - + -
106A PRO 2.8 13.9 + - - +
107A VAL* 3.4 8.0 - - + +
108A VAL 2.9 26.0 + - - +
126A ASP* 3.3 32.5 - - + -
127A LEU* 3.9 18.4 - - + -
200A LYS* 3.7 47.3 - - + -
201A ALA* 3.8 25.1 - - + +
204A ARG* 3.6 34.8 - - + +
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Residues in contact with VAL 8 (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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6A PRO 3.6 8.5 - - - +
7A PHE* 1.3 73.1 - - - +
9A ILE* 1.3 65.7 + - - +
78A LEU* 3.3 34.3 - - + -
108A VAL* 3.3 12.6 - - + +
110A LEU* 3.9 29.2 - - + -
124A LEU* 3.2 28.3 - - + +
125A MET* 4.0 10.3 - - + -
126A ASP* 2.7 37.6 + - - +
127A LEU 3.2 8.1 + - - +
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Residues in contact with ILE 9 (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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7A PHE* 3.4 37.9 - - + +
8A VAL* 1.3 75.6 - - - +
10A GLY* 1.3 65.7 + - - +
11A ILE* 3.8 26.2 - - + -
26A LEU* 4.5 17.3 - - + -
107A VAL* 4.4 7.4 - - + -
108A VAL 2.8 14.2 + - - +
109A ILE* 3.3 10.4 - - + +
110A LEU 2.9 27.1 + - - +
127A LEU* 3.5 25.1 - - + +
129A VAL* 4.3 5.2 - - + -
197A LEU* 4.7 5.4 - - + +
201A ALA* 4.1 17.3 - - + -
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Residues in contact with GLY 10 (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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9A ILE* 1.3 73.4 - - - +
11A ILE* 1.3 56.8 + - - +
12A ALA 4.0 0.7 - - - -
110A LEU* 3.3 8.1 - - - -
115A VAL* 4.7 2.2 - - - -
116A LEU* 5.0 2.0 - - - -
125A MET* 3.7 32.9 - - - +
127A LEU 2.9 10.4 + - - +
128A LYS* 3.6 0.6 - - - -
129A VAL* 2.7 36.2 + - - +
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Residues in contact with ILE 11 (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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9A ILE* 3.8 13.0 - - + -
10A GLY* 1.3 76.9 - - - +
12A ALA* 1.3 59.9 + - - +
19A LYS* 4.0 18.2 - - + +
22A LEU* 4.3 10.3 - - + -
23A ALA* 4.1 19.3 - - + +
26A LEU* 4.1 18.6 - - + -
109A ILE* 3.8 23.3 - - + -
110A LEU 2.8 9.5 + - - -
111A GLU* 3.3 11.8 - - + +
112A GLY 3.2 22.9 + - - -
115A VAL* 3.8 3.0 - - - +
129A VAL* 3.4 13.2 - - + -
131A VAL* 3.8 26.7 - - + -
197A LEU* 5.4 0.7 - - + -
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Residues in contact with ALA 12 (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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10A GLY 4.0 0.6 - - - -
11A ILE* 1.3 75.9 - - - +
13A GLY* 1.3 59.6 + - - +
19A LYS* 4.0 4.4 - - - +
112A GLY 3.3 14.8 - - - +
113A ILE 4.3 8.1 - - - +
115A VAL* 3.8 4.9 - - + +
116A LEU* 3.6 36.1 - - + +
129A VAL 2.7 8.2 + - - +
130A PHE* 3.4 8.0 - - + -
131A VAL* 2.8 30.7 + - - +
176A THR* 4.6 2.5 - - - +
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Residues in contact with GLY 13 (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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12A ALA* 1.3 79.9 - - - +
14A GLY* 1.3 68.0 + - - +
17A SER* 3.7 5.6 - - - -
19A LYS* 3.7 3.4 - - - +
112A GLY 3.8 1.2 + - - -
113A ILE* 3.2 25.6 + - - +
130A PHE* 3.9 11.7 - - - -
131A VAL 3.6 15.9 - - - -
173A VAL* 3.7 7.3 - - - +
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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