Contacts of the strand formed by residues 126 - 132 (chain A) in PDB entry 4GEK
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 ALA 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLN 3.2 10.8 - - - +
61A TYR* 3.9 28.0 - - + -
123A ILE* 4.0 9.6 - - + -
124A GLU 3.8 0.4 - - - -
125A ASN* 1.3 76.5 - - - +
127A SER* 1.3 59.4 + - - +
128A MET 4.2 0.9 - - - +
129A VAL* 4.0 12.8 - - + -
153A GLY 3.3 14.1 + - - +
154A LEU* 3.3 8.4 - - + +
155A ASN* 2.8 31.5 + - - +
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Residues in contact with SER 127 (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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53A PHE* 3.5 23.5 - - - +
54A VAL* 3.4 12.0 - - - +
55A GLN* 3.2 19.1 + - - -
58A THR* 2.7 28.6 + - - -
59A GLN 2.9 8.6 + - - -
60A VAL* 4.2 0.5 - - - +
125A ASN 3.9 2.0 + - - -
126A ALA* 1.3 74.0 - - - +
128A MET* 1.3 61.6 + - - +
154A LEU* 3.9 2.9 - - - -
155A ASN* 4.8 4.5 - - - +
158A GLY* 3.2 9.2 - - - -
159A ALA 3.0 20.1 + - - -
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Residues in contact with MET 128 (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 ILE* 3.5 41.1 - - + +
49A LEU* 4.1 22.4 - - + -
50A ALA* 3.8 26.2 - - - -
53A PHE* 4.9 4.9 - - + -
54A VAL* 4.2 8.1 - - + -
59A GLN 3.8 1.7 + - - +
60A VAL* 3.2 24.8 - - + -
61A TYR 3.0 21.5 + - - -
74A VAL* 4.0 7.6 - - + -
126A ALA* 3.4 1.9 - - - +
127A SER* 1.3 83.5 + - - +
129A VAL* 1.3 73.9 + - - +
130A VAL* 3.9 12.3 - - + -
154A LEU* 3.8 0.9 - - - +
159A ALA* 3.1 17.0 - - + +
161A VAL* 4.3 4.9 - - + -
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Residues in contact with VAL 129 (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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61A TYR* 3.4 17.5 - - + +
63A LEU* 3.7 29.6 - - + -
123A ILE* 4.2 9.6 - - + -
126A ALA* 4.0 12.6 - - + -
128A MET* 1.3 81.3 - - - +
130A VAL* 1.3 67.5 + - - +
150A ILE* 3.9 23.6 - - + -
154A LEU* 3.9 16.2 - - + -
159A ALA 2.9 8.5 + - - +
160A LEU* 3.2 18.1 - - + -
161A VAL 2.9 24.3 + - - -
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Residues in contact with VAL 130 (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 ILE* 4.1 18.2 - - + -
60A VAL* 5.0 2.7 - - + -
61A TYR 2.8 15.2 + - - +
62A ASP* 4.2 8.1 - - + +
63A LEU* 2.9 31.9 + - - +
70A ALA* 3.9 16.6 - - + -
74A VAL* 4.5 8.1 - - + -
128A MET* 3.9 28.3 - - + -
129A VAL* 1.3 79.4 - - - +
131A LEU* 1.3 64.5 + - - +
132A ASN* 3.6 27.4 - - + +
161A VAL* 3.6 11.7 - - + +
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Residues in contact with LEU 131 (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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63A LEU* 3.6 33.9 - - + -
118A ILE* 4.2 0.2 - - + -
130A VAL* 1.3 73.9 - - - +
132A ASN* 1.3 60.7 + - - +
133A PHE 3.3 3.6 + - - -
134A THR* 3.8 24.8 + - + -
135A LEU* 4.3 11.0 - - + +
146A LEU* 4.0 18.8 - - + -
147A LEU* 3.9 19.3 - - + -
150A ILE* 3.7 25.1 - - + -
160A LEU* 4.2 5.8 - - + +
161A VAL 2.8 13.7 + - - +
162A LEU* 3.6 18.6 - - + +
163A SER 2.9 25.1 + - - +
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Residues in contact with ASN 132 (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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39A TYR* 3.8 13.3 - - - -
42A ILE* 3.4 12.9 - - - +
43A ILE* 3.7 18.2 - - - +
46A ILE* 3.7 11.0 - - + +
63A LEU 4.4 0.8 + - - -
70A ALA* 4.5 1.6 - - + -
130A VAL* 3.6 19.4 + - + +
131A LEU* 1.3 70.2 - - - +
133A PHE* 1.3 77.6 + - - +
134A THR* 3.6 3.9 + - - -
163A SER* 2.7 30.9 + - - -
302A GEK 2.8 58.5 + - - +
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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