Contacts of the strand formed by residues 142 - 148 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A TRP* 4.0 10.8 - + - -
31A LYS* 3.8 33.9 - - + -
34A VAL* 3.9 28.7 - - + -
96A PHE* 3.5 35.9 - + + -
97A GLY 3.4 4.0 - - - -
98A SER* 5.1 5.4 - - - -
101A TYR* 3.6 4.9 - - - -
137A ILE* 3.3 13.3 - - - +
138A PRO* 3.3 17.1 - - + +
139A ALA* 3.1 31.9 + - + +
140A PRO 3.6 0.4 - - - -
141A HIS* 1.3 96.7 - - + +
143A SER* 1.3 59.0 + - - +
162A LEU* 4.9 3.1 - - + -
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 4.3 5.6 - - - -
96A PHE* 3.4 6.8 - - - -
97A GLY* 2.9 29.1 + - - +
101A TYR* 3.0 21.1 + - - -
136A SER 3.5 5.6 - - - -
137A ILE* 3.6 21.3 - - - -
138A PRO* 4.2 0.2 - - - -
142A PHE* 1.3 75.3 - - - +
144A CYS* 1.3 66.0 + - - +
145A VAL* 5.3 1.8 - - - -
301A MPD 2.8 29.7 + - - +
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Residues in contact with CYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 4.4 4.7 - - - -
95A LEU 3.4 4.9 - - - -
96A PHE* 3.8 23.1 - - - -
135A VAL* 3.3 4.5 - - - +
136A SER 2.8 35.9 + - - +
138A PRO* 4.1 9.9 - - - -
143A SER* 1.3 78.6 - - - +
145A VAL* 1.3 63.8 + - - +
155A MET* 3.7 20.7 - - - +
158A MET* 3.9 18.4 - - + -
159A LEU* 3.8 23.8 - - + -
162A LEU* 5.1 1.3 - - - -
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 4.7 2.5 - - + -
75A ILE* 5.3 1.8 - - + -
93A PHE 4.0 0.3 - - - +
94A ARG* 3.5 1.4 - - - -
95A LEU* 2.8 46.0 + - + +
133A THR* 3.8 25.8 - - + -
134A ASP 3.2 3.8 - - - -
135A VAL* 4.0 20.0 - - + -
143A SER* 5.3 0.7 - - - -
144A CYS* 1.3 80.3 - - - +
146A ILE* 1.3 68.1 + - - +
147A PHE 4.1 0.4 - - - +
158A MET* 4.6 0.3 - - - +
300A MPD 3.9 18.6 - - + -
301A MPD 3.5 39.9 - - + -
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Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLU* 3.9 12.1 - - - +
93A PHE 3.4 7.0 - - - +
94A ARG* 4.6 4.3 - - + -
132A HIS 3.8 0.7 - - - +
133A THR* 3.5 2.4 - - - +
134A ASP* 2.8 37.8 + - + +
145A VAL* 1.3 79.3 - - - +
147A PHE* 1.3 60.9 + - - +
152A ARG* 3.8 25.4 + - + +
153A GLU* 3.4 33.0 - - + +
154A ARG 4.0 1.6 - - - +
155A MET* 3.7 34.3 - - + -
158A MET* 3.6 32.5 - - + -
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Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 3.7 43.7 - + + -
67A GLU 6.0 0.7 - - - -
92A GLU* 3.2 3.1 - - - -
93A PHE* 2.8 49.9 + + + +
95A LEU* 5.4 0.4 - - + -
132A HIS* 3.2 26.9 - + + -
133A THR* 3.3 20.9 - - - +
145A VAL* 4.1 2.4 - - + -
146A ILE* 1.3 75.2 - - - +
148A GLY* 1.3 59.1 + - - +
152A ARG* 4.1 4.5 - - - -
281A TYR* 3.7 45.1 - + + -
300A MPD 3.7 38.4 - - + -
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Residues in contact with GLY 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS 3.6 3.4 - - - -
92A GLU* 4.3 0.7 - - - -
132A HIS* 2.9 31.7 + - - +
147A PHE* 1.3 80.0 - - - +
149A SER* 1.3 68.0 + - - +
152A ARG* 3.3 9.8 + - - +
281A TYR* 3.4 28.3 - - - -
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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