Contacts of the strand formed by residues 149 - 155 (chain B) in PDB entry 5HKE
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 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B THR* 4.3 6.5 + - - +
113B VAL* 4.5 2.0 - - - -
142B LEU* 3.9 12.7 - - - +
143B ILE 3.1 14.8 - - - -
144B ALA* 3.8 13.2 - - - -
148B LYS* 1.3 80.0 - - - +
150B ILE* 1.3 68.4 + - - +
163B ASP* 3.9 1.6 - - - +
164B ASN* 2.9 45.6 + - - +
167B GLY* 3.8 14.6 - - - -
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Residues in contact with ILE 150 (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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113B VAL* 3.7 26.2 - - + +
117B ARG* 4.0 34.1 - - + +
120B VAL* 5.6 0.4 - - + -
141B TRP 3.9 0.2 - - - +
142B LEU* 3.4 6.0 - - - +
143B ILE* 2.8 64.4 + - + +
148B LYS* 5.9 1.1 - - + -
149B SER* 1.3 80.2 - - - +
151B VAL* 1.3 65.0 + - - +
152B VAL* 4.5 4.5 - - + -
161B ILE* 3.8 20.0 - - + -
162B TYR 3.1 13.9 - - - +
163B ASP* 3.7 17.3 - - - +
164B ASN 4.3 0.7 - - - +
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Residues in contact with VAL 151 (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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141B TRP 3.3 8.5 - - - +
142B LEU* 4.1 4.3 - - + -
150B ILE* 1.3 76.5 - - - +
152B VAL* 1.3 65.5 + - - +
153B GLU* 3.9 25.4 - - + +
160B HIS 3.6 1.0 - - - +
161B ILE* 3.3 7.4 - - - +
162B TYR* 2.8 44.1 + - + +
164B ASN* 3.4 33.9 - - + +
169B LEU* 3.8 23.6 - - + -
175B PHE* 3.9 17.0 - - + -
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 4.2 14.4 - - + -
120B VAL* 3.9 33.0 - - + -
140B HIS* 3.4 7.3 - - - +
141B TRP* 2.9 44.2 + - + +
143B ILE* 3.9 27.6 - - + -
150B ILE* 4.5 9.9 - - + -
151B VAL* 1.3 76.1 - - - +
153B GLU* 1.3 64.5 + - - +
154B VAL* 4.1 19.3 - - + -
159B VAL* 4.8 0.7 - - + -
160B HIS 3.4 6.5 - - - +
161B ILE* 4.6 5.2 - - + -
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Residues in contact with GLU 153 (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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80B PHE* 3.5 20.6 - - + -
140B HIS* 2.6 44.6 + - + +
151B VAL* 3.9 8.5 - - + +
152B VAL* 1.3 74.9 - - - +
154B VAL* 1.3 59.8 + - - +
155B THR* 3.8 4.9 - - + -
160B HIS* 2.8 47.5 + - + +
162B TYR* 3.6 18.2 + - + +
173B PRO 4.5 0.2 - - - +
174B GLU* 3.5 10.7 - - - +
175B PHE* 2.9 42.1 + - - +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 4.7 2.1 - - - -
84B ALA* 3.4 9.9 - - - +
85B TYR* 2.9 42.5 + - + +
86B TYR* 5.6 1.3 - - + -
102B PHE* 5.5 0.7 - - + -
123B ILE* 5.4 2.7 - - + -
125B LEU* 3.8 39.0 - - + +
139B LEU 5.3 1.7 + - - +
141B TRP* 4.7 6.8 - - + -
152B VAL* 4.1 19.0 + - + -
153B GLU* 1.3 71.1 - - - +
155B THR* 1.3 65.5 + - - +
158B GLY 3.5 5.8 - - - +
159B VAL* 4.2 30.7 - - + -
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Residues in contact with THR 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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80B PHE* 4.0 15.3 - - + -
83B ASN 3.4 20.2 - - - +
85B TYR* 3.3 16.9 - - - +
153B GLU* 4.2 11.4 - - + +
154B VAL* 1.3 79.6 - - - +
156B LYS* 1.3 65.6 + - - +
157B SER* 3.1 10.4 + - - -
158B GLY* 3.0 17.1 + - - +
160B HIS* 3.2 10.8 + - + -
174B GLU* 3.7 14.1 - - + +
402B PO4 2.5 32.7 + - - +
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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