Contacts of the strand formed by residues 70 - 76 (chain A) in PDB entry 4KM9
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 TYR 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.1 27.8 - - + -
53A GLN* 3.8 27.4 - - - +
54A VAL 3.4 3.8 - - - -
55A THR* 3.1 32.8 + - - -
59A LYS* 4.5 12.5 + - - -
68A LEU* 4.6 0.7 - - - +
69A ASP* 1.3 94.3 - - + +
71A VAL* 1.3 67.1 + - - +
93A PHE* 2.9 49.0 + - + +
99A TYR* 4.5 8.3 - - - -
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Residues in contact with VAL 71 (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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53A GLN* 3.4 6.3 - - - +
54A VAL* 2.9 36.3 + - + +
68A LEU* 4.4 17.0 - - + -
70A TYR* 1.3 79.3 - - - +
72A SER* 1.3 67.0 + - - +
73A MET* 3.4 4.3 - - + +
90A TYR* 4.5 8.3 - - + -
91A ILE 3.3 13.2 - - - +
92A SER* 4.7 1.3 - - - -
138A ALA* 3.8 33.9 - - + +
141A MET* 4.0 18.4 - - - -
142A GLN* 4.4 18.6 - - - +
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Residues in contact with SER 72 (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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38A TYR* 5.2 2.8 - - - -
51A PRO* 4.5 3.9 - - - +
53A GLN* 2.8 33.1 + - - +
70A TYR 4.1 1.0 - - - -
71A VAL* 1.3 73.0 - - - +
73A MET* 1.3 60.3 + - - +
74A TYR* 3.7 28.6 + - - -
89A HIS 3.8 0.7 - - - +
90A TYR* 3.4 4.5 - - - -
91A ILE* 3.0 36.6 + - - +
93A PHE* 3.4 22.1 - - - -
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Residues in contact with MET 73 (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 GLN* 4.8 1.4 + - - -
51A PRO* 4.0 9.8 - - - +
52A LEU* 3.0 64.9 + - + +
53A GLN 4.7 0.2 - - - +
54A VAL* 3.8 23.3 - - + -
71A VAL* 3.4 14.4 - - + +
72A SER* 1.3 72.9 - - - +
74A TYR* 1.3 65.2 + - - +
89A HIS 3.3 6.1 - - - +
90A TYR* 3.7 32.5 - - + -
133A PRO* 3.9 25.4 - - + +
134A PRO 4.1 7.2 - - - +
135A THR* 4.0 17.9 - - + -
138A ALA* 4.8 1.6 - - - -
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Residues in contact with TYR 74 (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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38A TYR* 3.4 21.1 - - - -
41A CYS* 3.3 38.5 - - + +
42A ARG* 5.2 1.2 - - - +
45A TYR* 3.4 48.5 - + + -
48A GLN* 3.2 39.3 + - - +
51A PRO* 3.6 15.8 - - + +
72A SER* 3.7 24.3 + - - -
73A MET* 1.3 76.0 - - - +
75A ARG* 1.3 60.5 + - - +
88A TRP* 3.6 12.1 - - - +
89A HIS* 2.7 33.6 + - + +
91A ILE* 4.0 15.3 - - + -
133A PRO* 5.1 0.2 - - - +
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Residues in contact with ARG 75 (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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45A TYR* 3.3 11.9 - - - -
47A ASP* 4.7 1.4 - - - +
48A GLN* 2.9 33.6 - - - +
74A TYR* 1.3 75.7 - - - +
76A ASN* 1.3 68.1 + - - +
77A VAL* 4.2 5.6 + - + +
86A GLU* 4.1 23.8 + - + +
87A HIS 3.9 5.4 - - - +
88A TRP* 3.7 31.4 - - + -
126A ARG* 3.5 45.4 - - - +
130A GLU 4.9 0.2 + - - -
131A SER* 4.9 7.5 + - - +
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Residues in contact with ASN 76 (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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45A TYR* 2.9 30.2 + - - +
74A TYR 4.3 0.2 - - - -
75A ARG* 1.3 75.5 - - - +
77A VAL* 1.3 70.9 + - - +
78A GLY* 2.8 32.6 + - - +
86A GLU* 3.4 5.1 - - - +
87A HIS* 2.9 58.6 + - + +
89A HIS* 5.0 0.6 - - + +
123A ARG* 3.9 3.1 + - - -
184A GLN* 3.2 22.2 + - - +
233A TRP* 4.3 7.7 - - - -
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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