Contacts of the strand formed by residues 140 - 146 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LYS* 4.9 0.6 - - - +
91B THR* 3.1 25.4 - - - +
93B ILE* 3.8 27.9 - - + +
136B VAL* 4.3 3.6 - - + -
137B ASP* 2.9 34.8 + - - -
138B GLU 3.1 2.6 - - - +
139B ASP* 1.3 76.8 - - - +
141B PHE* 1.3 57.3 + - - +
142B LEU 4.1 7.2 - - - +
143B VAL* 4.3 3.1 - - + -
169B ASN* 3.6 7.8 + - - -
171B GLU 5.3 0.3 - - - -
172B THR* 2.6 43.9 + - + +
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B VAL* 4.1 6.5 - - + -
82B ALA* 3.7 33.0 - - + -
85B PHE* 3.6 41.0 - + + -
89B LYS* 3.4 31.0 - - + -
90B ARG* 3.9 8.3 - - - -
91B THR 3.1 15.1 + - - -
92B ILE* 3.6 20.6 - - + -
114B PHE* 3.7 22.7 - + - -
140B THR* 1.3 73.3 - - - +
142B LEU* 1.3 79.8 + - + +
171B GLU 4.4 2.3 - - - +
172B THR* 3.6 7.9 - - - +
173B LEU* 2.8 28.8 + - - +
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 4.9 2.0 - - + +
78B LEU* 3.7 37.2 - - + +
81B VAL* 4.4 16.8 - - + -
91B THR 3.9 1.2 + - - -
92B ILE* 3.5 19.2 - - + +
93B ILE 3.0 23.6 + - - -
140B THR* 3.7 2.0 - - - +
141B PHE* 1.3 102.6 - - + +
143B VAL* 1.3 72.7 + - - +
144B SER* 4.2 0.9 - - - +
172B THR* 3.8 0.8 - - - +
173B LEU* 3.3 32.8 - - + +
174B VAL 4.2 1.1 - - - +
175B HIS* 4.3 13.0 - - + +
196B TYR* 4.5 9.2 - - + -
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.1 34.3 - - + +
94B THR* 5.5 0.7 - - - -
132B LEU* 4.9 4.0 - - + -
136B VAL* 4.6 2.9 - - + -
140B THR* 4.3 5.4 - - + -
142B LEU* 1.3 77.7 - - - +
144B SER* 1.3 67.5 + - - +
145B ILE* 4.6 5.2 - - + +
161B VAL* 4.5 21.3 - - + -
165B VAL* 4.2 18.8 - - + -
172B THR* 3.9 15.5 - - + -
173B LEU 2.8 12.5 + - - +
174B VAL* 3.4 12.7 - - + +
175B HIS* 2.9 25.6 + - - +
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Residues in contact with SER 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 4.0 11.2 - - - +
93B ILE 2.7 9.5 + - - -
94B THR* 2.5 33.9 + - - -
95B THR 4.1 0.5 + - - -
98B GLU* 4.1 3.3 + - - +
102B VAL* 4.1 11.8 - - - +
106B MET* 3.7 26.9 - - - -
142B LEU* 4.2 2.6 + - - +
143B VAL* 1.3 71.5 - - - +
145B ILE* 1.3 61.3 + - - +
175B HIS* 2.9 34.0 + - - -
177B ASP* 5.8 0.3 - - - +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR* 3.4 31.9 - - + +
97B ILE* 5.6 0.9 - - + -
98B GLU* 3.4 9.6 - - - +
127B VAL* 5.0 5.6 - - + -
143B VAL* 4.8 4.7 - - + -
144B SER* 1.3 75.4 + - - +
146B MET* 1.3 79.5 + - + +
156B GLN* 4.3 20.9 - - + +
158B VAL* 5.1 8.5 - - + -
161B VAL* 4.1 33.9 - - + -
174B VAL* 4.5 8.7 - - + -
175B HIS 3.0 9.4 + - - +
176B VAL* 3.1 22.6 - - + -
177B ASP* 3.0 20.3 + - - -
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Residues in contact with MET 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ILE* 3.5 26.7 - - + +
98B GLU* 3.2 22.7 + - - +
99B HIS 3.7 23.6 - - - +
145B ILE* 1.3 83.7 - - + +
147B ALA* 1.3 59.0 + - - +
148B ALA 3.7 19.1 - - - +
149B ASN* 3.9 12.3 - - - +
150B ASN* 3.8 10.3 - - - +
156B GLN* 3.0 36.7 - - + +
158B VAL* 4.3 1.3 - - - +
176B VAL* 4.5 1.6 - - - -
177B ASP* 3.4 16.8 - - + +
501B PLP 3.7 27.6 - - + -
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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