Contacts of the strand formed by residues 140 - 146 (chain A) in PDB entry 1ECX
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 THR 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A LYS* 4.8 0.9 - - - -
91A THR* 3.1 24.2 - - - +
93A ILE* 3.5 31.9 - - + +
135A LEU 4.2 0.3 + - - -
136A VAL* 4.5 2.9 - - + -
137A ASP* 3.1 30.5 + - - -
138A GLU 3.2 1.6 - - - +
139A ASP* 1.3 77.4 - - - +
141A PHE* 1.3 57.1 + - - +
142A LEU 3.9 9.0 - - - +
143A VAL* 4.0 1.6 - - + -
169A ASN* 4.0 5.7 + - - -
172A THR* 2.6 48.9 + - + +
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Residues in contact with PHE 141 (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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81A VAL* 3.8 11.2 - - + -
82A ALA* 3.6 22.4 - - + -
85A PHE* 3.6 42.5 - + + -
89A LYS* 3.5 24.7 - - + -
90A ARG* 3.8 2.2 - - - -
91A THR 3.0 36.6 + - - -
92A ILE* 3.3 27.6 - - + -
114A PHE* 3.8 25.4 - + - -
139A ASP 3.4 0.4 + - - -
140A THR* 1.3 73.6 - - - +
142A LEU* 1.3 72.4 + - + +
171A GLU 4.6 1.6 - - - +
172A THR* 3.7 6.0 - - - +
173A LEU* 2.9 31.0 + - - +
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Residues in contact with LEU 142 (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* 5.3 1.3 - - + -
78A LEU* 3.4 37.7 - - + +
81A VAL* 4.3 17.3 - - + -
91A THR 3.8 0.8 + - - -
92A ILE* 3.3 21.2 - - + +
93A ILE 2.9 23.0 + - - -
106A MET* 5.1 0.4 - - + -
140A THR* 3.6 3.1 - - - +
141A PHE* 1.3 99.2 - - + +
143A VAL* 1.3 69.2 + - - +
172A THR* 4.0 0.4 - - - -
173A LEU* 3.2 31.2 - - + +
175A HIS* 4.2 20.2 - - + -
196A TYR* 4.3 10.8 - - + -
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Residues in contact with VAL 143 (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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93A ILE* 3.2 28.9 - - + +
94A THR* 5.2 1.1 - - - -
132A LEU* 4.8 6.3 - - + -
136A VAL* 4.5 0.9 - - + -
140A THR* 4.0 9.2 - - + -
142A LEU* 1.3 80.1 - - - +
144A SER* 1.3 67.3 + - - +
145A ILE* 5.0 4.9 - - + +
161A VAL* 5.0 10.5 - - + -
165A VAL* 4.0 26.2 - - + -
172A THR* 3.5 20.4 - - + -
173A LEU 2.8 10.6 + - - +
174A VAL* 3.4 12.1 - - + +
175A HIS* 2.9 25.5 + - - +
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Residues in contact with SER 144 (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 LEU* 4.0 10.0 - - - +
93A ILE 2.8 9.5 + - - -
94A THR* 2.5 34.8 + - - -
95A THR 4.1 0.2 + - - -
98A GLU* 3.7 4.5 + - - +
102A VAL* 4.0 11.7 - - - +
106A MET* 3.7 27.6 - - - -
142A LEU* 4.3 0.8 - - - -
143A VAL* 1.3 72.9 - - - +
145A ILE* 1.3 60.9 + - - +
175A HIS* 2.9 32.7 + - - -
177A ASP* 5.9 0.2 - - - +
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Residues in contact with ILE 145 (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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95A THR* 3.4 23.6 - - + +
97A ILE* 5.8 0.7 - - + -
98A GLU* 3.2 17.0 - - - +
127A VAL* 5.0 4.3 - - + -
143A VAL* 5.1 5.4 - - + +
144A SER* 1.3 75.8 + - - +
146A MET* 1.3 81.2 + - + +
156A GLN* 4.3 20.4 - - + +
158A VAL* 5.2 7.6 - - + -
161A VAL* 4.3 33.0 - - + -
174A VAL* 4.6 8.1 - - + -
175A HIS 3.0 10.0 + - - +
176A VAL* 3.1 26.6 - - + +
177A ASP 3.0 19.3 + - - -
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Residues in contact with MET 146 (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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97A ILE* 3.2 38.6 - - + +
98A GLU* 3.0 22.2 + - - +
99A HIS 4.2 8.3 - - - +
145A ILE* 1.3 79.3 - - + +
147A ALA* 1.3 59.7 + - - +
148A ALA 3.5 24.0 - - - +
149A ASN* 3.6 11.4 - - - +
150A ASN* 3.6 25.4 - - - +
156A GLN* 2.8 38.0 - - + +
158A VAL* 4.5 0.8 - - - +
176A VAL* 4.4 0.9 - - - -
177A ASP* 3.5 16.6 - - + +
500A PLP 3.7 14.8 - - + -
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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