Contacts of the helix formed by residues 158 - 172 (chain A) in PDB entry 2YVE
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 SER 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A VAL* 3.5 4.3 + - - -
157A LEU* 1.3 76.2 - - - +
159A LYS* 1.3 59.9 - - - +
160A SER* 3.4 10.2 + - - -
161A LYS* 2.8 48.3 + - - +
162A ARG* 2.8 28.2 + - - +
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Residues in contact with LYS 159 (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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158A SER* 1.3 74.2 - - - +
160A SER* 1.3 58.4 + - - +
162A ARG* 3.3 10.8 + - + +
163A GLN* 2.9 38.9 + - + +
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Residues in contact with SER 160 (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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158A SER* 3.3 9.0 + - - -
159A LYS* 1.3 79.6 - - - +
161A LYS* 1.3 58.1 + - - +
163A GLN* 3.4 7.8 + - - +
164A ALA* 3.1 26.5 + - - +
128B GLU* 2.6 36.2 + - - +
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Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP* 5.0 2.8 + - - +
156A VAL 3.3 15.4 + - - -
157A LEU* 3.4 26.5 - - + +
158A SER* 2.8 49.4 + - - +
160A SER* 1.3 73.6 - - - +
162A ARG* 1.3 61.1 + - - +
164A ALA* 3.3 4.5 + - - +
165A MET* 3.0 32.9 + - - +
124B THR* 3.7 33.3 + - - +
125B ASP* 5.8 0.4 - - - -
127B LEU* 4.2 8.7 - - + +
128B GLU* 3.7 24.7 - - - +
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Residues in contact with ARG 162 (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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89A ALA* 2.8 40.2 + - + +
90A GLU* 4.9 2.0 - - - +
91A ASN* 2.8 41.2 + - - +
146A LEU* 2.9 36.9 + - + +
149A HIS* 3.7 7.7 - - - +
150A ASP* 2.9 24.0 + - - -
157A LEU* 3.0 35.9 + - + +
158A SER 2.8 18.2 + - - +
159A LYS* 3.6 8.5 - - + +
161A LYS* 1.3 76.1 - - - +
163A GLN* 1.3 58.1 + - - +
165A MET* 3.3 1.2 + - - +
166A LEU* 2.8 32.0 + - - +
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Residues in contact with GLN 163 (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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159A LYS* 2.9 30.0 + - + +
160A SER* 3.5 9.4 - - - +
161A LYS 3.2 0.2 - - - -
162A ARG* 1.3 76.3 - - - +
164A ALA* 1.3 62.5 + - - +
166A LEU* 3.3 24.0 + - - +
167A GLU* 3.0 52.9 + - - +
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Residues in contact with ALA 164 (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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160A SER 3.1 16.8 + - - +
161A LYS* 3.7 4.9 - - - +
162A ARG 3.3 0.2 - - - -
163A GLN* 1.3 77.2 - - - +
165A MET* 1.3 62.1 + - + +
167A GLU* 3.3 12.8 + - - +
168A THR* 3.0 25.9 + - - -
127B LEU* 4.2 2.2 - - + +
128B GLU* 3.9 29.2 - - + +
134B ARG* 3.9 16.4 + - + +
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Residues in contact with MET 165 (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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146A LEU* 4.4 8.7 - - + -
157A LEU* 4.8 3.1 - - + -
161A LYS 3.0 21.4 + - - +
162A ARG 3.9 2.9 - - - +
164A ALA* 1.3 73.0 - - - +
166A LEU* 1.3 61.4 + - - +
168A THR* 3.1 9.9 + - - -
169A ILE* 2.8 36.5 + - - +
127B LEU* 3.9 26.5 - - + -
134B ARG* 3.4 38.4 - - - +
137B TYR* 3.9 19.1 - - + -
138B LEU* 3.6 22.9 - - + +
141B LEU* 3.8 26.5 - - + -
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Residues in contact with LEU 166 (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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85A VAL* 3.5 36.3 - - + +
86A VAL* 3.9 22.9 - - + -
89A ALA* 4.0 20.6 - - + -
146A LEU* 4.2 6.9 - - + +
162A ARG 2.8 22.0 + - - +
163A GLN* 3.3 27.8 + - - +
165A MET* 1.3 70.9 - - - +
167A GLU* 1.3 65.2 + - + +
169A ILE* 3.2 4.4 + - - +
170A LEU* 3.0 42.5 + - + +
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Residues in contact with GLU 167 (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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163A GLN* 3.0 49.5 + - - +
164A ALA* 3.6 10.2 - - - +
165A MET 3.2 0.2 - - - -
166A LEU* 1.3 77.7 - - + +
168A THR* 1.3 58.5 + - - +
170A LEU* 3.4 9.0 + - + +
171A GLU* 3.0 36.8 + - - +
2005A GOL 4.1 25.4 + - - +
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Residues in contact with THR 168 (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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164A ALA 3.0 14.3 + - - -
165A MET* 3.1 17.0 + - + -
167A GLU* 1.3 73.9 - - - +
169A ILE* 1.3 63.5 + - - +
171A GLU* 3.2 32.9 + - - +
172A LEU* 3.4 7.6 + - - +
134B ARG* 3.2 46.6 + - + +
135B ALA* 5.0 1.6 - - - +
138B LEU* 4.2 21.9 - - + +
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Residues in contact with ILE 169 (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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85A VAL* 3.7 20.4 - - + -
139A VAL* 3.8 31.1 - - + +
142A ALA* 3.8 28.9 - - + +
143A ALA* 4.0 4.0 - - - +
146A LEU* 4.0 22.4 - - + -
165A MET* 2.8 20.7 + - + +
166A LEU* 3.2 4.7 + - - +
168A THR* 1.3 76.1 - - - +
170A LEU* 1.3 64.5 + - - +
172A LEU* 3.0 20.3 + - + +
173A ILE* 3.7 6.2 + - - +
138B LEU* 3.7 24.2 - - + -
141B LEU* 4.3 8.7 - - + -
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Residues in contact with LEU 170 (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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82A ARG* 3.8 46.3 + - + +
85A VAL* 4.0 11.4 - - + -
86A VAL* 4.6 9.4 - - + -
166A LEU* 3.0 39.2 + - + +
167A GLU* 3.8 4.5 - - + +
169A ILE* 1.3 76.4 - - - +
171A GLU* 1.3 62.4 + - - +
173A ILE* 3.2 32.4 + - + +
2005A GOL 3.3 35.5 + - - +
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Residues in contact with GLU 171 (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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167A GLU* 3.0 28.4 + - - +
168A THR* 3.3 25.9 + - - +
169A ILE 3.1 0.4 - - - -
170A LEU* 1.3 76.4 - - + +
172A LEU* 1.3 60.9 + - - +
173A ILE 3.3 6.3 + - - +
2005A GOL 5.6 6.7 - - - -
134B ARG* 5.3 7.1 + - - -
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Residues in contact with LEU 172 (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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135A ALA* 5.0 2.7 - - - +
138A LEU* 4.0 33.4 - - + +
139A VAL* 3.9 23.0 - - + +
142A ALA* 5.1 1.1 - - + -
168A THR 3.4 6.8 + - - +
169A ILE* 3.0 14.0 + - - +
171A GLU* 1.3 80.1 - - - +
173A ILE* 1.3 62.4 + - - +
174A PRO* 3.4 7.4 - - - +
138B LEU* 3.9 33.2 - - + -
172B LEU* 4.1 22.0 - - + -
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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