Contacts of the strand formed by residues 164 - 175 (chain B) in PDB entry 1D2G
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 VAL 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B GLY* 4.2 1.2 - - - -
130B PHE 3.8 6.5 - - - +
133B VAL* 3.4 22.4 - - + -
160B ILE 4.0 5.4 - - - +
161B ALA* 3.1 18.1 + - - +
162B SER 4.1 2.6 - - - +
163B MET* 1.3 78.9 - - - +
165B ARG* 1.3 64.2 + - - +
166B PRO* 4.3 0.3 - - - +
168B GLY* 3.3 36.3 - - - +
169B LEU 3.4 14.1 - - - +
170B LEU* 4.2 13.2 - - + -
258B PHE* 4.6 4.3 - - + -
290B LYS* 3.0 37.6 + - + +
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Residues in contact with ARG 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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55B HIS 5.1 8.3 + - - -
56B GLY 5.3 3.0 + - - -
57B CYS* 5.8 1.8 - - - -
128B ASP 3.1 25.8 - - - +
129B GLY* 3.5 6.5 - - - -
130B PHE 3.4 22.7 + - - +
131B ASP* 2.9 37.5 + - - +
164B VAL* 1.3 77.7 - - - +
166B PRO* 1.3 91.6 + - + +
167B GLY* 3.7 16.6 + - - -
168B GLY* 2.6 37.7 + - - -
290B LYS* 3.8 1.8 - - - +
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Residues in contact with PRO 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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128B ASP 4.4 4.9 - - - +
164B VAL 4.3 2.0 - - - +
165B ARG* 1.3 115.5 + - + +
167B GLY* 1.3 52.9 + - - +
290B LYS* 3.9 16.6 - - + +
291B THR 4.8 2.2 - - - +
292B GLY* 3.6 24.9 - - - +
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Residues in contact with GLY 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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165B ARG* 3.7 14.6 + - - -
166B PRO* 1.3 72.0 - - - +
168B GLY* 1.3 62.7 + - - +
169B LEU* 5.0 0.9 - - - +
289B LYS* 2.9 34.3 + - - -
290B LYS 2.6 20.5 + - - -
291B THR 4.4 2.7 + - - -
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Residues in contact with GLY 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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131B ASP 3.3 13.0 - - - -
164B VAL* 3.3 9.6 - - - -
165B ARG* 2.6 28.0 + - - -
166B PRO 3.0 1.6 + - - -
167B GLY* 1.3 83.0 - - - +
169B LEU* 1.3 60.3 + - - -
289B LYS* 3.4 6.2 - - - +
290B LYS 3.1 23.2 + - - -
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Residues in contact with LEU 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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51B LEU* 3.9 37.2 - - + +
52B LEU* 4.4 6.3 - - + -
55B HIS* 3.5 37.7 - - + +
57B CYS* 4.3 12.6 - - - -
131B ASP 2.8 14.8 + - - +
132B ALA* 3.3 7.7 - - + -
133B VAL 2.9 24.1 + - - -
164B VAL* 3.4 12.1 - - - +
167B GLY 5.0 0.4 - - - +
168B GLY* 1.3 77.7 - - - +
170B LEU* 1.3 61.2 + - - +
171B VAL* 4.2 5.4 - - + -
287B VAL* 4.5 13.0 - - + -
288B LEU 3.4 11.4 - - - +
289B LYS* 4.1 14.1 - - + +
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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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133B VAL* 3.4 23.8 - - + +
134B ILE* 5.3 0.7 - - - -
135B CYS* 5.5 2.2 - - + -
157B LEU* 5.7 3.6 - - + +
160B ILE* 3.7 30.3 - - + -
161B ALA* 4.9 5.4 - - + -
164B VAL* 4.2 5.6 - - + -
169B LEU* 1.3 73.8 - - - +
171B VAL* 1.3 62.0 + - - +
172B ILE* 4.4 20.6 - - + -
254B VAL* 4.2 17.9 - - + -
258B PHE* 3.5 41.1 - - + -
286B HIS 3.2 4.9 - - - +
287B VAL* 3.3 1.4 - - - -
288B LEU* 2.9 39.8 + - + +
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Residues in contact with VAL 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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47B TRP* 3.3 37.0 - - + -
48B LEU* 4.6 4.5 - - + -
51B LEU* 3.8 22.2 - - + -
52B LEU* 5.0 4.0 - - + -
132B ALA* 5.5 0.9 - - + -
133B VAL 2.9 7.9 + - - +
134B ILE* 3.5 20.6 - - + -
135B CYS 3.0 24.6 + - - -
136B LEU* 3.6 11.7 - - + +
169B LEU* 4.6 14.1 - - + -
170B LEU* 1.3 74.8 - - - +
172B ILE* 1.3 57.6 + - - +
285B ILE* 3.9 12.6 - - + -
286B HIS 3.5 3.1 - - - +
287B VAL* 4.4 5.6 - - + +
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Residues in contact with ILE 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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135B CYS* 3.6 33.4 - - + +
136B LEU* 4.7 1.1 - - - -
140B PHE* 4.1 23.1 - - + -
157B LEU* 4.2 16.2 - - + -
160B ILE* 4.9 5.8 - - + -
170B LEU* 4.4 17.9 - - + -
171B VAL* 1.3 74.3 - - - +
173B ASP* 1.3 67.4 + - - +
250B PHE* 4.0 17.9 - - + -
254B VAL* 4.1 13.9 - - + -
285B ILE* 4.7 0.4 - - - -
286B HIS* 2.7 56.1 + - + +
288B LEU* 4.7 0.7 - - + -
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Residues in contact with ASP 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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135B CYS 3.4 9.4 + - - +
136B LEU* 4.0 6.3 - - + -
137B GLY 3.4 10.7 + - - -
138B ASN* 2.9 26.7 + - - -
140B PHE* 4.5 10.6 + - - +
141B ALA 5.5 0.3 + - - -
172B ILE* 1.3 86.0 - - - +
174B HIS* 1.3 70.3 + - - +
193B TYR* 2.6 38.3 + - - +
250B PHE* 4.6 1.9 - - - -
283B TYR* 3.8 6.2 - - + -
284B PHE 3.1 15.5 - - - +
285B ILE* 3.9 9.0 - - + -
286B HIS* 4.5 1.8 - - - +
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Residues in contact with HIS 174 (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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138B ASN* 3.5 12.3 - - - +
140B PHE* 6.2 0.4 - - + -
141B ALA* 5.5 2.5 - - + +
173B ASP* 1.3 80.3 - - - +
175B LYS* 1.3 87.7 + - - +
176B ASN* 4.8 0.2 - - - -
177B TYR* 4.8 2.0 - - + -
245B HIS* 3.7 31.2 + - + +
247B LEU* 4.0 12.4 + - + -
250B PHE* 3.4 34.2 - + + -
283B TYR* 3.6 6.6 - - - -
284B PHE* 2.8 50.7 + + + +
286B HIS* 2.9 35.8 + + - -
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Residues in contact with LYS 175 (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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138B ASN* 3.1 22.3 + - - +
174B HIS* 1.3 92.4 - - - +
176B ASN* 1.3 60.2 + - - +
177B TYR* 2.9 32.8 + - + +
180B ILE* 4.2 18.4 - - + -
186B ALA* 5.7 5.8 - - + -
187B PRO* 5.0 13.5 - - - -
190B LYS* 5.3 5.8 - - - +
191B ASN 5.1 4.2 - - - +
218B LEU* 6.2 4.5 - - + -
282B CYS* 3.5 21.1 - - - +
283B TYR* 2.7 48.3 + - + -
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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