Contacts of the strand formed by residues 154 - 159 (chain B) in PDB entry 2HDH
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 PHE 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B PHE* 3.4 39.9 - + + -
132B PHE* 3.3 25.1 - + + -
134B SER* 4.6 7.6 - - - -
141B ILE* 3.9 22.9 - - + -
144B ILE* 3.4 34.1 - - + -
145B ALA* 3.4 31.9 - - + -
148B THR* 4.2 8.3 - - + -
150B ARG* 3.2 7.2 + - + +
151B GLN* 3.2 12.3 + - - +
152B ASP 3.4 0.2 - - - -
153B ARG* 1.3 80.0 - - - +
155B ALA* 1.3 89.1 + - - +
174B THR* 4.5 2.4 + - - +
177B THR* 2.8 24.4 + - - +
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Residues in contact with ALA 155 (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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132B PHE 3.0 6.8 + - - +
133B ALA* 3.3 5.4 - - - -
134B SER 3.2 19.4 + - - -
141B ILE* 3.7 11.7 - - - +
154B PHE* 1.3 84.8 - - - +
156B GLY* 1.3 61.9 + - - +
171B VAL* 5.5 2.0 - - + -
172B ILE 3.5 12.1 - - - +
173B LYS* 5.1 0.2 - - - -
177B THR* 4.1 15.0 - - + -
181B THR* 4.5 2.0 - - + -
182B PHE* 6.2 0.2 - - - -
185B LEU* 3.5 29.8 - - + -
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Residues in contact with GLY 156 (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 ALA* 4.8 0.2 - - - -
134B SER 3.5 7.9 - - - -
141B ILE* 3.7 13.1 - - - +
155B ALA* 1.3 79.2 - - - +
157B LEU* 1.3 63.5 + - - +
158B HIS 4.0 1.1 - - - -
171B VAL* 3.6 6.6 - - - +
172B ILE* 2.8 48.9 + - - +
185B LEU* 4.5 0.7 - - - +
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Residues in contact with LEU 157 (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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105B VAL* 4.3 16.1 - - + +
133B ALA* 4.0 14.4 - - + -
134B SER 2.8 9.2 + - - +
135B ASN* 3.1 25.3 - - - +
155B ALA 4.2 0.4 + - - -
156B GLY* 1.3 75.3 - - - +
158B HIS* 1.3 59.1 + - - +
159B PHE* 3.6 31.7 - - + -
169B VAL* 3.6 20.0 - - + -
170B GLU 3.6 0.9 - - - -
171B VAL* 4.0 15.9 - - + -
185B LEU* 4.3 22.7 - - + -
188B PHE* 4.2 24.2 - - + -
189B SER* 3.9 14.1 - - - +
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Residues in contact with HIS 158 (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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134B SER 5.3 0.4 - - - +
135B ASN* 3.4 17.0 - - - +
136B THR 3.3 24.5 - - - +
137B SER* 2.8 27.9 + - - -
157B LEU* 1.3 72.2 - - - +
159B PHE* 1.3 74.0 + - - +
160B PHE* 3.5 23.8 - + - -
169B VAL* 3.4 5.2 - - - -
170B GLU* 2.9 64.0 + - + +
172B ILE* 4.9 1.1 - - + -
205B PHE* 3.9 18.8 - + + -
208B ASN* 3.9 14.9 + - - -
750B NAD 4.2 5.2 - + - -
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Residues in contact with PHE 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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26B MSE 3.3 25.2 - - + +
30B ILE* 3.7 32.3 - - + -
33B VAL* 6.2 0.7 - - + -
105B VAL* 4.5 2.2 - - + -
135B ASN* 2.8 17.5 + - - -
157B LEU* 3.6 43.1 - - + -
158B HIS* 1.3 90.2 + - - +
160B PHE* 1.3 69.8 + - - +
163B VAL* 3.8 29.2 - - + -
168B LEU 4.3 3.6 - - - -
169B VAL* 4.1 17.0 - - + -
188B PHE* 5.0 0.7 - + - -
189B SER* 5.9 0.2 - - - -
192B LEU* 3.7 30.3 - - + -
194B LYS* 4.6 12.3 - - + -
750B NAD 4.0 2.8 - - - -
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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