Contacts of the strand formed by residues 175 - 181 (chain A) in PDB entry 4EJX
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 ILE 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A TYR* 3.6 4.6 - - - -
73A PHE* 3.7 11.2 - - + -
74A LEU* 3.3 28.6 - - + +
75A GLY 3.1 16.3 + - - -
159A ILE* 4.3 13.7 - - + -
160A TYR 3.6 6.1 - - - +
161A HIS* 3.9 29.2 - - + -
170A ILE* 4.2 16.8 - - + +
173A GLY 2.8 19.6 + - - +
174A LEU* 1.3 73.9 - - - +
176A GLY* 1.3 60.5 + - - +
201A MET* 4.1 18.4 - - - -
267A PHE* 4.8 8.5 - - + -
269A MET* 4.2 23.8 - - + -
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Residues in contact with GLY 176 (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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74A LEU* 5.2 0.2 - - - -
75A GLY 3.5 10.1 - - - -
159A ILE* 3.3 4.6 - - - +
160A TYR* 2.5 66.9 + - - +
175A ILE* 1.3 75.8 - - - +
177A PRO* 1.3 66.9 - - - +
267A PHE* 5.1 0.9 - - - -
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Residues in contact with PRO 177 (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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71A LEU* 4.5 4.9 - - + -
74A LEU* 4.2 11.4 - - + -
75A GLY 3.2 20.0 - - - +
76A PRO 4.4 1.1 - - - +
77A ILE* 4.4 4.6 - - + +
78A ILE 3.5 14.4 + - - -
158A ARG 3.5 7.4 - - - +
159A ILE* 4.0 1.6 - - - -
160A TYR* 3.3 12.4 - - - -
176A GLY* 1.3 84.5 - - - +
178A LEU* 1.3 61.0 + - - +
179A ILE* 4.7 5.9 - - + +
199A VAL* 3.5 33.4 - - + -
267A PHE* 3.5 28.3 - - + -
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Residues in contact with LEU 178 (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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78A ILE* 3.2 35.4 - - + +
80A ALA* 4.0 10.3 - - + +
100A PHE* 5.3 1.3 - - + -
102A SER* 4.2 24.2 - - - -
103A HIS 4.3 10.3 - - - +
105A ILE* 4.3 19.5 - - + -
140A LEU* 4.9 3.4 - - + -
158A ARG* 2.7 46.1 + - + +
159A ILE* 3.7 7.2 - - - +
160A TYR* 4.5 5.4 - - + -
177A PRO* 1.3 74.6 - - - +
179A ILE* 1.3 85.6 + - - +
180A ILE* 3.7 24.9 - - + -
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Residues in contact with ILE 179 (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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77A ILE* 4.5 12.3 - - + -
78A ILE 2.6 14.1 + - - +
79A LYS* 3.4 28.2 - - + -
80A ALA 3.3 18.0 + - - -
155A CYS* 3.9 11.7 - - + -
156A VAL 3.8 10.3 - - - +
157A THR* 4.9 3.4 - - + -
158A ARG 5.0 0.4 - - - +
177A PRO* 4.7 9.2 - - + +
178A LEU* 1.3 84.6 - - - +
180A ILE* 1.3 60.2 + - - +
181A CYS* 3.4 25.1 - - - -
199A VAL* 4.5 12.3 - - + -
265A TYR* 3.9 42.2 - - + -
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Residues in contact with ILE 180 (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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80A ALA* 3.7 29.6 - - + +
104A GLY 3.8 18.4 - - - +
105A ILE* 4.1 12.8 - - + -
142A ALA* 4.3 11.0 - - + -
146A GLN 3.9 16.2 - - - +
147A SER* 4.1 4.3 - - - -
148A PRO* 3.8 20.0 - - + -
156A VAL* 2.7 44.6 + - + +
158A ARG* 3.5 28.4 - - + +
178A LEU* 3.7 15.3 + - + -
179A ILE* 1.3 71.1 - - - +
181A CYS* 1.3 61.2 + - - +
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Residues in contact with CYS 181 (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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79A LYS* 5.0 2.7 - - - -
80A ALA 3.2 17.0 + - - +
81A GLU* 4.0 2.4 - - + -
82A THR* 3.4 12.5 + - - -
142A ALA* 5.7 0.3 - - - +
147A SER* 4.7 0.5 - - - -
148A PRO* 3.7 10.5 - - - +
154A ASN 3.1 8.3 - - - +
155A CYS* 2.0 49.6 - - - -
179A ILE* 3.4 19.3 - - - +
180A ILE* 1.3 78.8 - - - +
182A LYS* 1.3 70.2 + - - +
185A SER* 4.9 0.9 - - - -
186A LEU* 4.0 19.1 - - + -
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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