Contacts of the strand formed by residues 92 - 99 (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 GLU 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ALA 3.9 0.2 - - - +
86A PHE* 3.3 11.1 - - - -
87A PHE* 2.9 37.6 + - + -
90A SER* 2.6 32.7 + - - +
91A LYS* 1.3 75.3 - - - +
93A PHE* 1.3 61.7 + - - +
94A ARG* 3.0 43.4 + - + +
146A ILE* 3.9 2.1 - - - +
147A PHE 3.2 11.9 - - - +
148A GLY* 4.3 0.4 - - - -
151A LYS 4.2 0.5 - - - +
152A ARG* 3.6 15.6 - - + +
153A GLU* 2.9 30.0 + - - +
281A TYR* 5.1 0.7 - - - -
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Residues in contact with PHE 93 (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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48A LEU* 4.4 19.5 - - + -
66A HIS* 4.3 5.4 - + - -
85A ALA 3.3 8.5 - - - -
86A PHE* 3.8 35.0 - + + -
92A GLU* 1.3 74.9 - - - +
94A ARG* 1.3 62.7 + - - +
95A LEU* 4.2 17.9 - - + +
145A VAL 4.0 0.3 - - - +
146A ILE* 3.4 4.7 - - - +
147A PHE* 2.8 48.5 + + + +
277A ILE* 3.9 23.6 - - + -
280A LEU* 4.0 12.1 - - + -
281A TYR* 3.7 26.9 - + + -
300A MPD 3.7 33.7 - - + -
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Residues in contact with ARG 94 (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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40A VAL* 3.3 32.7 + - + +
41A GLY* 4.4 2.8 - - - -
42A SER 5.0 1.2 + - - -
84A GLY* 3.3 2.4 - - - -
85A ALA 2.8 34.0 + - - +
87A PHE* 3.2 41.9 - - + -
90A SER* 4.6 0.8 + - - -
92A GLU* 3.0 39.4 + - - +
93A PHE* 1.3 77.5 - - - +
95A LEU* 1.3 61.8 + - - +
145A VAL 3.5 4.5 - - - -
146A ILE* 4.6 6.3 - - + -
153A GLU* 3.3 37.9 + - - +
158A MET* 4.3 12.3 - - - -
161A ARG* 3.4 15.3 - - - +
166A ASP* 5.6 0.2 + - - -
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Residues in contact with LEU 95 (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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40A VAL* 4.0 2.7 - - - -
48A LEU* 5.9 1.3 - - + -
50A PHE* 6.2 2.7 - - + -
82A VAL* 4.1 12.8 - - + -
83A TYR 3.2 3.8 - - - +
84A GLY* 3.7 21.8 - - - -
93A PHE* 4.5 19.5 - - + +
94A ARG* 1.3 80.8 - - - +
96A PHE* 1.3 61.4 + - - +
144A CYS* 3.4 5.5 - - - -
145A VAL* 2.8 50.4 + - + +
147A PHE* 5.4 0.2 - - + -
158A MET* 3.5 4.5 - - - +
300A MPD 4.0 38.6 - - + +
301A MPD 3.4 26.6 - - + +
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Residues in contact with PHE 96 (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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34A VAL* 3.9 16.6 - - + -
36A PRO* 3.4 37.2 - - + +
39A VAL* 3.8 20.9 - - + -
40A VAL* 3.7 18.4 - - + +
82A VAL* 3.4 1.1 - - - -
83A TYR* 2.8 46.7 + + + +
95A LEU* 1.3 75.1 - - - +
97A GLY* 1.3 69.2 + - - +
98A SER* 4.0 7.6 - - - -
142A PHE* 3.5 40.6 - + + -
143A SER 3.4 4.0 - - - -
144A CYS* 3.8 12.6 - - - -
158A MET* 4.5 1.1 - - + -
162A LEU* 4.1 22.7 - - + -
301A MPD 3.7 2.5 - - - -
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Residues in contact with GLY 97 (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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79A THR* 4.1 1.6 - - - -
81A ALA 3.3 8.1 - - - -
82A VAL* 4.5 0.9 - - - -
96A PHE* 1.3 80.6 - - - +
98A SER* 1.3 63.1 + - - -
101A TYR* 3.8 5.5 + - - -
142A PHE* 3.4 5.9 - - - -
143A SER* 2.9 42.1 + - - +
301A MPD 3.3 13.5 - - - +
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Residues in contact with SER 98 (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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36A PRO* 4.8 2.1 - - - +
79A THR* 3.4 4.0 - - - +
80A THR* 2.7 42.2 + - - -
81A ALA* 3.0 10.6 + - - -
83A TYR* 3.9 17.8 + - - -
96A PHE* 4.0 10.3 + - - -
97A GLY* 1.3 72.3 - - - -
99A GLY* 1.3 53.0 + - - +
101A TYR* 3.8 1.6 - - - -
141A HIS 3.4 8.1 - - - -
142A PHE* 5.1 4.3 - - - -
181A GLU* 4.4 13.3 + - - -
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Residues in contact with GLY 99 (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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78A ARG 3.3 14.6 - - - -
79A THR* 4.0 0.9 - - - -
80A THR* 4.1 9.6 - - - -
98A SER* 1.3 75.6 - - - +
100A SER* 1.3 60.5 + - - -
101A TYR* 3.7 12.3 - - - -
141A HIS* 3.0 37.0 + - - +
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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