Contacts of the helix formed by residues 158 - 173 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLU* 3.9 1.0 + - - -
156B VAL* 3.6 4.4 + - - -
157B LEU* 1.3 78.7 - - - +
159B LYS* 1.3 65.2 + - - +
160B SER* 3.2 20.0 + - - -
161B LYS* 3.1 28.0 + - - +
162B ARG* 2.9 18.9 + - - +
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Residues in contact with LYS 159 (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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90B GLU* 5.5 8.3 + - - +
157B LEU 3.8 1.7 + - - -
158B SER* 1.3 74.2 - - - +
160B SER* 1.3 57.3 + - - +
162B ARG* 3.4 30.1 + - - +
163B GLN* 3.0 30.0 + - + +
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 2.6 33.1 + - - +
158B SER* 3.2 10.9 + - - -
159B LYS* 1.3 76.7 - - - +
161B LYS* 1.3 58.2 + - - +
163B GLN* 3.5 6.1 + - - +
164B ALA* 3.0 28.4 + - - +
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Residues in contact with LYS 161 (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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124A THR* 2.9 50.3 + - - +
125A ASP* 4.2 7.3 + - - +
126A ASP 4.3 3.1 - - - +
127A LEU* 3.9 10.9 - - + +
128A GLU* 3.3 33.0 - - + +
156B VAL 6.0 0.2 - - - +
157B LEU* 4.0 17.0 - - + -
158B SER* 3.1 26.7 + - - +
160B SER* 1.3 74.8 + - - +
162B ARG* 1.3 61.0 + - - +
164B ALA* 3.3 4.0 + - - +
165B MET* 3.0 34.7 + - - +
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Residues in contact with ARG 162 (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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89B ALA* 2.7 44.1 + - + +
90B GLU* 4.5 4.9 - - - +
91B ASN* 3.6 21.9 - - - +
146B LEU* 3.0 42.4 + - + +
149B HIS* 4.3 1.6 - - - +
150B ASP* 3.2 37.2 + - - -
157B LEU* 4.0 28.7 + - + +
158B SER 2.9 15.3 + - - +
159B LYS* 3.7 28.6 - - - +
161B LYS* 1.3 78.4 - - - +
163B GLN* 1.3 56.5 + - - +
165B MET* 3.2 2.9 + - - +
166B LEU* 2.9 27.3 + - + +
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Residues in contact with GLN 163 (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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159B LYS* 3.0 18.3 + - + +
160B SER* 3.8 7.4 - - - +
162B ARG* 1.3 76.7 - - - +
164B ALA* 1.3 64.4 + - - +
166B LEU* 3.2 24.7 + - - +
167B GLU* 2.9 58.3 + - - +
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Residues in contact with ALA 164 (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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127A LEU* 3.6 19.3 - - + -
128A GLU* 4.2 13.5 - - + +
134A ARG* 4.2 10.3 - - - -
160B SER 3.0 18.9 + - - +
161B LYS 3.3 5.1 + - - +
163B GLN* 1.3 78.7 - - - +
165B MET* 1.3 57.6 + - - +
167B GLU* 3.4 12.8 + - - +
168B THR* 2.8 31.5 + - - -
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Residues in contact with MET 165 (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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127A LEU* 3.6 35.9 - - + -
134A ARG* 3.7 18.8 - - - +
137A TYR* 3.9 11.7 - - + -
138A LEU* 3.6 33.4 - - + +
141A LEU* 3.7 30.3 - - + -
146B LEU* 4.3 12.6 - - + -
157B LEU* 5.1 3.6 - - + -
161B LYS 3.0 20.0 + - - +
162B ARG 3.2 3.6 + - - +
164B ALA* 1.3 73.9 - - - +
166B LEU* 1.3 65.0 + - - +
168B THR* 3.2 12.8 + - + -
169B ILE* 2.9 30.1 + - - +
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Residues in contact with LEU 166 (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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85B VAL* 3.6 29.4 - - + +
86B VAL* 4.3 15.9 - - + +
89B ALA* 3.8 32.8 - - + -
146B LEU* 3.9 8.6 - - + +
162B ARG 2.9 13.5 + - - +
163B GLN* 3.2 31.6 + - - +
165B MET* 1.3 74.6 - - - +
167B GLU* 1.3 58.8 + - - +
169B ILE* 3.2 4.5 + - - +
170B LEU* 2.9 49.8 + - + +
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Residues in contact with GLU 167 (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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2003A GOL 4.9 5.1 + - - +
163B GLN* 2.9 53.5 + - - +
164B ALA* 3.6 10.3 - - - +
166B LEU* 1.3 76.2 - - + +
168B THR* 1.3 62.1 + - - +
170B LEU* 3.3 13.0 + - + +
171B GLU* 3.0 24.1 + - - +
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Residues in contact with THR 168 (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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134A ARG* 3.5 27.1 + - - +
138A LEU* 4.0 27.0 - - + +
2003A GOL 2.8 41.7 + - - +
164B ALA 2.8 19.4 + - - -
165B MET* 3.5 14.5 - - + -
167B GLU* 1.3 76.4 - - - +
169B ILE* 1.3 61.0 + - - +
171B GLU* 3.4 4.9 + - - +
172B LEU* 3.4 18.5 + - - +
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Residues in contact with ILE 169 (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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138A LEU* 3.8 20.4 - - + -
141A LEU* 4.3 7.6 - - + -
85B VAL* 3.8 16.8 - - + -
139B VAL* 3.8 33.0 - - + +
142B ALA* 3.6 31.6 - - + +
143B ALA* 3.9 4.9 - - + +
146B LEU* 4.0 22.0 - - + -
165B MET* 2.9 21.4 + - + +
166B LEU* 3.7 4.0 - - - +
168B THR* 1.3 74.3 - - - +
170B LEU* 1.3 60.4 + - - +
172B LEU* 2.9 28.8 + - + +
173B ILE* 3.6 5.9 + - - +
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Residues in contact with LEU 170 (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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82B ARG* 3.9 47.1 + - + +
85B VAL* 3.8 22.2 - - + -
86B VAL* 4.6 7.6 - - + -
166B LEU* 2.9 42.2 + - + +
167B GLU* 3.8 10.5 - - + +
169B ILE* 1.3 75.9 - - - +
171B GLU* 1.3 60.9 + - - +
172B LEU 3.3 0.7 + - - -
173B ILE* 3.3 39.8 + - + +
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Residues in contact with GLU 171 (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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2003A GOL 4.4 22.0 - - - +
167B GLU 3.0 16.1 + - - +
168B THR 3.7 6.7 - - - +
169B ILE 3.1 0.4 - - - -
170B LEU* 1.3 76.8 - - - +
172B LEU* 1.3 59.9 + - - +
173B ILE 3.3 7.7 + - - +
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Residues in contact with LEU 172 (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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138A LEU* 3.8 35.0 - - + -
172A LEU* 4.1 21.8 - - + -
135B ALA* 4.8 2.2 - - - +
138B LEU* 4.1 31.4 - - + +
139B VAL* 3.7 22.2 - - + +
142B ALA* 4.8 2.2 - - + -
168B THR 3.4 9.0 + - - +
169B ILE* 2.9 13.6 + - - +
171B GLU* 1.3 77.4 - - - +
173B ILE* 1.3 63.0 + - - +
174B PRO* 3.4 8.5 - - - +
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Residues in contact with ILE 173 (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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78B LEU* 4.3 20.6 - - + +
81B LEU* 4.0 15.5 - - + -
82B ARG* 4.0 29.2 - - + +
85B VAL* 4.7 0.7 - - + -
139B VAL* 3.9 23.1 - - + -
169B ILE 4.1 2.0 - - - +
170B LEU* 3.4 39.8 - - + +
171B GLU 3.3 8.3 - - - +
172B LEU* 1.3 79.7 - - - +
174B PRO* 1.3 79.6 - - + +
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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