Contacts of the strand formed by residues 113 - 122 (chain A) in PDB entry 5I2Y
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 ARG 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ARG* 5.1 10.9 + - - +
97A PRO 5.2 0.6 + - - -
98A TRP* 3.6 65.1 - - + +
101A GLU* 5.1 8.5 + - - -
102A LEU* 5.4 4.8 - - + +
109A PRO* 5.3 8.8 - - + +
111A SER* 3.8 23.3 + - - +
112A PRO* 1.3 80.1 - - - +
114A ALA* 1.3 59.6 + - - +
183A LEU* 3.8 3.6 - - - -
184A LEU* 2.8 46.9 + - + +
213B PRO* 3.3 31.2 - - - +
214B THR* 5.2 2.2 + - - +
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Residues in contact with ALA 114 (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 LEU* 3.6 40.6 - - + +
98A TRP* 2.7 30.4 + - - +
113A ARG* 1.3 73.6 - - - +
115A GLY* 1.3 55.0 + - - +
181A LEU* 5.2 1.3 - - + -
182A LEU 3.5 6.7 - - - +
183A LEU* 3.8 16.8 - - + +
212A LEU* 4.9 11.2 - - + -
93B LEU* 4.8 2.3 - - - +
212B LEU* 5.3 5.4 - - + -
213B PRO* 6.1 0.2 - - - +
214B THR* 5.9 0.9 - - - +
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Residues in contact with GLY 115 (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 LEU* 4.9 0.6 - - - +
98A TRP* 4.6 4.9 - - - -
113A ARG 4.0 0.4 + - - -
114A ALA* 1.3 74.8 - - - +
116A GLN* 1.3 58.3 + - - -
146A VAL* 4.2 13.2 - - - -
147A SER 3.3 12.6 - - - -
181A LEU* 3.6 3.9 - - - -
182A LEU* 2.7 46.0 + - - +
184A LEU* 5.6 0.6 - - - +
93B LEU* 4.0 8.7 - - - -
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Residues in contact with GLN 116 (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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115A GLY* 1.3 72.6 - - - -
117A LEU* 1.3 69.8 + - - +
118A LEU* 3.4 16.7 + - - +
146A VAL* 3.3 6.0 - - - +
147A SER* 2.7 44.0 + - - +
179A GLY* 3.2 13.6 + - - +
180A ARG 3.5 13.0 - - - +
181A LEU* 4.0 6.5 - - + -
216A GLN* 2.9 36.3 + - - +
217A PRO 3.1 16.9 + - - +
218A ARG* 3.7 10.2 - - - +
219A LEU 4.4 2.3 + - - -
93B LEU* 3.7 29.8 - - + +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLY 3.9 1.0 + - - -
116A GLN* 1.3 73.1 - - - +
118A LEU* 1.3 57.9 + - - +
119A GLU 3.4 28.7 - - - +
120A VAL* 4.5 3.6 - - + -
144A LEU* 3.6 29.8 - - + -
145A LEU 3.9 2.9 - - - +
146A VAL* 4.7 4.5 - - + -
174A PHE* 4.1 24.7 - - + +
177A THR* 3.1 38.6 - - - +
178A GLU* 4.3 4.5 - - - -
179A GLY* 2.8 32.2 + - - -
180A ARG* 2.9 18.1 + - + +
182A LEU* 4.8 12.5 - - + +
211A LEU* 5.9 1.6 - - + -
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Residues in contact with LEU 118 (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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116A GLN* 3.4 25.5 + - - +
117A LEU* 1.3 72.6 - - - +
119A GLU* 1.3 59.3 + - + +
145A LEU* 2.8 31.6 + - + +
147A SER* 3.6 28.9 - - - +
152A SER* 4.2 18.8 - - - -
178A GLU* 3.9 8.8 - - - +
218A ARG* 3.0 49.9 + - + +
219A LEU 4.4 16.6 - - - +
221A VAL* 5.0 7.4 - - + +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A LEU* 3.4 10.5 - - - +
118A LEU* 1.3 81.1 - - + +
120A VAL* 1.3 75.0 + - - +
121A LEU* 3.6 21.9 - - + +
144A LEU* 3.5 0.7 - - - -
145A LEU* 2.8 48.8 + - + +
178A GLU* 4.6 4.7 - - - -
218A ARG* 5.5 1.3 - - - +
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Residues in contact with VAL 120 (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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117A LEU* 4.5 4.0 - - + -
119A GLU* 1.3 83.7 - - - +
121A LEU* 1.3 62.5 + - - +
122A GLN 3.7 19.7 - - - +
123A ASP* 3.7 26.9 - - + +
143A THR 4.0 1.8 - - - -
144A LEU* 3.9 14.1 - - + -
174A PHE* 3.7 30.3 - - + +
175A ARG* 3.8 22.0 - - + +
178A GLU* 3.9 17.3 + - + +
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Residues in contact with LEU 121 (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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119A GLU* 3.6 34.1 - - + +
120A VAL* 1.3 75.6 - - - +
122A GLN* 1.3 63.0 + - + +
123A ASP 4.3 0.2 - - - -
143A THR* 2.9 33.1 + - + +
144A LEU 4.2 12.6 - - - +
145A LEU* 4.3 17.7 - - + +
154A ARG* 4.3 14.8 - - + -
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Residues in contact with GLN 122 (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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120A VAL* 3.7 6.1 - - - +
121A LEU* 1.3 80.7 + - - +
123A ASP* 1.3 78.1 + - - +
140A VAL* 5.3 8.3 - - + -
141A GLY 4.4 9.9 - - - +
142A ALA* 3.4 3.3 - - - -
143A THR* 2.7 48.1 + - - +
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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