Contacts of the strand formed by residues 142 - 148 (chain B) in PDB entry 3K8G
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 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B TRP* 4.3 13.0 - + - -
31B LYS* 3.4 29.6 - - + -
32B ALA 5.6 0.2 - - - -
34B VAL* 3.9 21.1 - - + -
96B PHE* 3.4 36.3 - + + -
97B GLY 3.4 2.9 - - - -
98B SER* 5.0 4.7 - - - -
101B TYR* 3.6 4.4 - - - -
137B ILE* 3.5 9.2 - - - +
138B PRO* 3.4 23.6 - - + +
139B ALA* 3.1 40.1 + - + +
140B PRO 3.7 0.4 - - - -
141B HIS* 1.3 99.7 - - + +
143B SER* 1.3 59.4 + - - +
162B LEU* 4.8 5.2 - - + -
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Residues in contact with SER 143 (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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75B ILE* 4.2 12.3 - - - -
96B PHE* 3.5 5.5 - - - -
97B GLY* 2.9 29.7 + - - +
101B TYR* 3.0 23.6 + - - -
135B VAL* 5.5 0.7 - - - -
136B SER 3.4 9.0 - - - -
137B ILE* 4.4 9.0 - - - -
138B PRO* 4.3 0.2 - - - -
142B PHE* 1.3 74.4 - - - +
144B CYS* 1.3 66.6 + - - +
145B VAL* 5.4 1.3 - - - -
302B MPD 2.8 29.2 + - - -
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Residues in contact with CYS 144 (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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39B VAL* 4.4 5.6 - - - -
95B LEU 3.4 4.5 - - - -
96B PHE* 4.1 22.0 - - - -
135B VAL* 3.3 5.2 - - - +
136B SER* 2.9 43.9 + - - +
138B PRO* 4.1 9.6 - - - -
143B SER* 1.3 80.1 - - - +
145B VAL* 1.3 63.2 - - - +
155B MET* 3.5 13.7 - - - +
158B MET* 4.0 17.7 - - + -
159B LEU* 3.7 22.4 - - - -
162B LEU* 5.3 1.1 - - - -
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Residues in contact with VAL 145 (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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72B ILE* 4.8 6.3 - - + -
75B ILE* 5.5 1.1 - - + -
93B PHE 3.9 0.5 - - - +
94B ARG* 3.3 2.8 - - - +
95B LEU* 2.7 60.2 + - + +
133B THR* 4.2 17.9 - - + -
134B ASP 3.3 7.9 - - - +
135B VAL* 4.1 19.3 - - + -
143B SER* 5.4 0.9 - - - -
144B CYS* 1.3 79.2 - - - +
146B ILE* 1.3 70.7 + - - +
147B PHE* 4.7 6.5 - - + +
158B MET* 4.6 0.7 - - - +
302B MPD 3.6 36.1 - - + -
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Residues in contact with ILE 146 (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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92B GLU* 3.8 20.6 - - - +
93B PHE 3.4 6.7 - - - +
94B ARG* 4.4 4.5 - - + -
132B HIS 3.9 0.5 - - - +
133B THR* 3.4 2.1 - - - +
134B ASP* 2.8 43.5 + - + +
145B VAL* 1.3 79.2 - - - +
147B PHE* 1.3 63.0 + - - +
152B ARG* 3.8 17.3 - - + -
153B GLU* 3.2 35.9 - - + +
154B ARG 4.0 0.9 - - - +
155B MET* 3.8 31.6 - - + +
158B MET* 3.7 31.2 - - + -
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Residues in contact with PHE 147 (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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92B GLU* 3.3 4.2 - - - +
93B PHE* 2.8 55.2 + + + +
95B LEU* 6.2 1.6 - - + -
132B HIS* 3.3 24.5 - + + -
133B THR* 3.3 30.1 - - + +
145B VAL* 4.2 7.6 - - + -
146B ILE* 1.3 75.4 - - - +
148B GLY* 1.3 59.7 + - - +
152B ARG* 4.0 4.3 - - - -
281B TYR* 3.6 43.1 - + + -
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Residues in contact with GLY 148 (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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91B LYS 3.5 8.1 - - - -
92B GLU* 4.3 0.9 - - - -
132B HIS* 2.8 29.0 + - - +
147B PHE* 1.3 81.2 - - - +
149B SER* 1.3 68.5 + - - +
152B ARG* 3.4 13.1 + - - +
281B TYR* 3.5 22.2 - - - -
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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