Contacts of the strand formed by residues 154 - 159 (chain D) in PDB entry 4K9P
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 154 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LEU 2.9 15.4 + - - +
93D ILE* 3.8 12.8 - - + -
94D VAL* 3.0 30.8 + - - +
123D VAL* 4.2 4.3 - - - -
124D LYS* 3.9 14.8 - - + -
125D TRP* 3.4 17.7 - - + +
142D ALA* 3.4 32.5 - - + +
145D MET* 3.9 13.0 - - + -
146D ALA* 3.7 25.4 - - + +
153D PRO* 1.3 79.3 - - - +
155D TYR* 1.3 61.0 + - - +
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Residues in contact with TYR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D THR* 2.8 42.0 + - + +
82D LEU* 5.7 2.2 - - + -
94D VAL* 3.5 24.2 - - + -
96D ALA* 3.4 18.4 - - + +
112D ASN* 3.1 20.4 + - - -
115D ALA 3.5 23.3 - - - -
116D ALA* 4.6 2.0 - - - -
118D LEU* 4.4 0.6 - - + +
119D PRO* 3.3 23.6 - - + -
123D VAL* 4.4 4.0 - - + -
125D TRP* 2.6 17.5 + - - +
126D SER* 3.0 30.0 - - - +
127D TYR* 3.0 25.7 + - - +
154D VAL* 1.3 76.7 - - - +
156D LEU* 1.3 67.8 + - - +
157D SER* 4.5 12.7 - - - -
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ILE* 6.0 0.4 - - + -
94D VAL 2.9 11.2 + - - +
95D THR* 3.2 10.1 - - + -
96D ALA* 3.0 26.2 + - - +
125D TRP* 4.9 1.8 - - + -
127D TYR* 3.3 23.6 - - + +
129D PRO* 3.9 13.9 - - + -
135D VAL* 4.8 2.9 - - + +
138D ALA* 3.9 25.4 - - + +
139D MET* 3.6 51.1 - - + +
142D ALA* 4.7 9.2 - - + -
155D TYR* 1.3 79.4 - - - +
157D SER* 1.3 60.6 + - - +
158D VAL* 3.9 16.0 + - + +
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Residues in contact with SER 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ALA 3.4 7.6 + - - +
98D GLN* 3.4 16.6 + - - +
112D ASN* 4.8 2.6 + - - -
115D ALA* 3.9 16.1 - - - +
116D ALA* 6.2 0.2 - - - -
127D TYR 3.0 11.9 + - - -
128D GLU* 2.6 33.5 + - - +
129D PRO* 3.0 26.2 - - - +
155D TYR* 4.5 13.4 - - - -
156D LEU* 1.3 73.0 - - - +
158D VAL* 1.3 61.2 + - - +
159D PRO 4.2 0.2 - - - -
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D THR* 5.6 4.3 - - - -
96D ALA 3.1 10.7 + - - +
97D GLY* 3.6 5.9 - - - -
98D GLN* 2.9 19.5 + - - -
129D PRO* 4.8 1.1 - - + -
135D VAL* 4.0 29.8 - - + -
139D MET* 5.4 0.7 - - + -
156D LEU* 3.9 28.5 - - + +
157D SER* 1.3 79.0 + - - +
159D PRO* 1.3 80.5 - - + +
160D TYR* 3.3 2.3 + - - -
162D ASP* 4.0 4.0 - - + -
163D TRP* 3.5 39.6 + - + -
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Residues in contact with PRO 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLN* 3.5 17.0 - - + +
99D GLN 3.3 20.4 - - - +
101D ARG* 3.8 35.7 - - + +
104D ILE* 4.4 4.3 - - + -
128D GLU* 4.5 8.7 - - + +
129D PRO* 5.0 1.6 - - + -
157D SER 3.9 6.7 - - - +
158D VAL* 1.3 88.8 - - - +
160D TYR* 1.3 66.1 + - - +
161D ASP* 3.2 13.0 - - - +
162D ASP* 3.0 36.7 + - - +
163D TRP* 4.3 0.2 + - - -
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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