Contacts of the strand formed by residues 133 - 140 (chain A) in PDB entry 2K1S
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 ARG 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ASN* 3.1 30.7 + - + +
32A MET 4.1 12.3 - - - +
33A PRO* 5.4 2.4 - - + +
34A ASN* 5.0 1.8 - - - +
72A GLY* 3.8 0.3 - - - -
73A TYR* 2.7 43.2 + - + +
90A ARG* 4.4 3.7 + - - +
119A ILE* 3.6 34.6 - - - +
130A GLN* 2.9 38.4 + - - +
131A ASN 3.0 8.8 + - - +
132A ARG* 1.3 75.0 - - - +
134A VAL* 1.3 70.3 + - - +
135A GLU* 2.7 34.6 + - + +
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Residues in contact with VAL 134 (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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30A LEU 3.5 2.3 - - - +
31A ASN* 3.3 0.7 - - - -
32A MET* 2.8 46.1 + - + +
34A ASN* 6.4 0.7 - - - -
37A THR* 5.4 2.9 - - + +
38A PHE* 3.5 33.7 - - + -
70A VAL* 4.1 16.4 - - + -
71A ILE 4.0 6.1 - - - +
72A GLY* 4.8 5.6 - - - -
90A ARG* 4.1 18.4 - - + +
91A ALA* 5.1 1.3 - - - -
94A VAL* 4.1 22.9 - - + -
133A ARG* 1.3 80.5 - - - +
135A GLU* 1.3 64.6 + - - +
136A ILE* 4.0 5.3 + - + +
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Residues in contact with GLU 135 (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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29A ILE* 4.0 22.5 - - + +
30A LEU 3.5 3.8 - - - -
31A ASN* 3.3 15.7 + - + +
71A ILE* 3.0 38.5 + - - +
73A TYR* 3.3 31.9 + - + -
119A ILE* 4.0 10.5 - - - +
133A ARG* 2.7 40.9 + - + +
134A VAL* 1.3 75.5 - - - +
136A ILE* 1.3 63.8 + - - +
137A THR* 3.4 6.6 + - - +
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Residues in contact with ILE 136 (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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28A ILE 3.3 5.4 - - - +
29A ILE* 3.6 1.1 - - - -
30A LEU* 2.8 56.6 + - + +
32A MET* 4.5 17.7 - - - -
53A LEU* 4.7 3.4 - - + -
56A VAL* 4.5 22.4 - - + -
68A VAL* 4.0 19.1 - - + -
69A ASN 3.8 4.3 - - - +
70A VAL* 4.6 9.4 - - + +
94A VAL* 3.9 29.2 - - + -
98A LEU* 5.4 1.3 - - + -
134A VAL* 4.8 6.5 - - + +
135A GLU* 1.3 70.5 - - - +
137A THR* 1.3 59.3 + - - +
138A LEU* 3.4 27.6 + - + +
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Residues in contact with THR 137 (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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27A ASN* 3.8 9.2 - - - +
28A ILE 3.7 3.1 - - - -
29A ILE* 3.5 26.6 - - + +
67A ALA 3.1 4.3 - - - +
68A VAL 4.1 0.3 - - - -
69A ASN* 2.8 46.1 + - + +
71A ILE* 3.7 20.2 - - + +
73A TYR* 6.1 0.2 - - - -
135A GLU* 3.4 5.9 + - - +
136A ILE* 1.3 70.1 - - - +
138A LEU* 1.3 60.5 + - - +
139A SER* 3.5 20.3 + - - +
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Residues in contact with LEU 138 (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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3A MET* 3.2 14.4 - - + +
6A GLN* 5.1 8.5 - - - +
10A LEU* 4.3 14.4 - - + -
27A ASN* 3.2 2.9 - - - +
28A ILE* 2.8 46.9 + - + +
30A LEU* 3.7 25.8 - - + -
56A VAL* 5.1 2.5 - - + -
59A VAL* 5.9 2.7 - - + -
60A LEU* 3.7 33.2 - - + -
66A THR* 4.9 5.6 - - + -
67A ALA 3.7 2.7 - - - +
68A VAL* 4.1 15.3 - - + -
136A ILE* 3.8 24.5 - - + +
137A THR* 1.3 71.9 - - - +
139A SER* 1.3 61.1 + - - +
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Residues in contact with SER 139 (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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3A MET* 3.6 3.6 - - - -
27A ASN* 3.5 15.8 - - - +
66A THR* 3.6 2.1 - - - -
67A ALA* 2.7 46.2 + - - +
69A ASN* 5.9 1.4 - - - +
137A THR* 3.5 16.5 + - - +
138A LEU* 1.3 76.4 - - - +
140A PRO* 1.3 72.6 - - - +
142A LEU* 4.9 8.3 - - - -
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Residues in contact with PRO 140 (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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2A TYR* 5.2 9.6 - - + -
3A MET* 3.6 24.0 - - + -
26A ASP* 4.8 13.9 - - + +
27A ASN* 4.8 6.1 - - + -
65A LYS 3.6 7.9 - - - +
67A ALA* 4.7 0.2 - - - +
139A SER* 1.3 88.2 - - - +
141A LEU* 1.3 67.0 + - - +
142A LEU* 2.9 21.9 + - + +
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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