Contacts of the strand formed by residues 114 - 122 (chain A) in PDB entry 5TKM
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 VAL 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A PHE* 4.5 5.4 - - + -
80A LEU* 5.4 1.3 - - + -
86A PHE* 3.5 24.0 - - + +
88A ILE* 3.6 31.6 - - + -
107A PHE* 4.0 22.0 - - + -
108A LEU* 3.8 15.7 - - + +
111A HIS* 3.1 29.0 + - + +
112A PRO* 4.0 4.3 - - - +
113A ASN* 1.3 93.3 - - - +
115A THR* 1.3 73.2 - - - +
116A LEU* 5.4 0.2 - - + -
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Residues in contact with THR 115 (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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42A LYS* 5.8 0.5 - - - +
86A PHE 3.0 13.7 + - - +
87A GLN* 3.6 18.6 - - - +
88A ILE* 2.8 29.3 + - - +
108A LEU* 4.6 2.0 - - - -
112A PRO 5.3 4.0 - - - +
113A ASN 5.6 1.3 - - - -
114A VAL* 1.3 81.5 - - - +
116A LEU* 1.3 63.3 + - - +
117A THR* 6.1 0.2 - - - -
142A GLY 5.6 5.4 - - - +
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Residues in contact with LEU 116 (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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88A ILE* 3.3 33.2 - - + +
90A TRP* 3.9 30.3 - - + +
104A LEU* 4.7 14.8 - - + -
107A PHE* 6.5 0.7 - - + -
108A LEU* 4.2 26.5 - - + +
115A THR* 1.3 77.2 - - - +
117A THR* 1.3 74.6 + - - +
118A ILE* 3.8 26.9 - - + -
138A LEU* 5.1 0.7 - - + -
142A GLY 4.5 1.7 + - - +
143A ALA* 3.3 16.9 - - + +
144A ARG* 3.0 22.9 + - - +
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Residues in contact with THR 117 (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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87A GLN* 5.3 7.1 - - - +
88A ILE 2.8 13.2 + - - +
89A THR* 3.5 16.1 + - + +
90A TRP* 2.8 31.9 + - - +
115A THR* 6.1 0.3 - - - -
116A LEU* 1.3 77.0 + - - +
118A ILE* 1.3 67.9 + - - +
119A SER* 4.3 9.9 - - - +
144A ARG* 3.3 35.5 - - + +
146A LYS* 4.5 7.2 - - + -
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Residues in contact with ILE 118 (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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90A TRP* 3.7 37.5 - - + -
92A VAL* 3.7 26.9 - - + -
95A THR* 5.2 3.1 - - + -
96A PRO* 4.1 16.4 - - + -
104A LEU* 4.7 0.7 - - + -
116A LEU* 3.8 20.2 - - + -
117A THR* 1.3 76.6 - - - +
119A SER* 1.3 62.9 + - - +
120A ALA* 4.1 4.7 - - + +
138A LEU* 3.8 30.3 - - + -
143A ALA* 5.3 1.3 - - + -
144A ARG 2.7 13.9 + - - +
145A VAL* 4.4 9.4 - - + +
146A LYS* 2.9 29.3 + - - +
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Residues in contact with SER 119 (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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89A THR* 5.7 1.0 - - - +
90A TRP 3.0 14.3 + - - -
91A PHE* 3.3 10.3 - - - -
92A VAL* 2.9 25.7 + - - +
117A THR* 4.1 6.1 - - - +
118A ILE* 1.3 71.4 - - - +
120A ALA* 1.3 59.9 + - - +
146A LYS* 3.3 23.2 - - - +
148A MET* 3.4 18.2 - - - +
152A GLU* 2.7 30.9 + - - -
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Residues in contact with ALA 120 (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 VAL* 3.2 16.6 - - + +
95A THR* 3.4 34.1 - - + +
118A ILE* 4.9 1.6 - - + -
119A SER* 1.3 74.5 - - - +
121A ALA* 1.3 63.9 + - - +
122A ARG 3.6 11.4 - - - +
145A VAL* 6.2 0.2 - - + -
146A LYS 3.0 11.7 + - - +
147A ILE* 3.6 11.0 - - + +
148A MET* 2.8 26.5 + - - +
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Residues in contact with ALA 121 (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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21A PHE* 3.4 41.3 - - + +
23A ASN* 3.3 22.3 - - - +
92A VAL 2.8 13.8 + - - +
93A SER* 3.8 10.3 - - - +
120A ALA* 1.3 74.8 - - - +
122A ARG* 1.3 63.2 + - + +
147A ILE* 4.7 1.7 - - - +
148A MET* 3.9 2.9 - - - -
153A PHE* 4.0 17.5 - - + -
181A LEU* 3.3 11.6 - - - +
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Residues in contact with ARG 122 (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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20A ASN* 2.8 30.9 + - - +
21A PHE* 3.9 2.6 - - - +
22A GLU 2.8 35.3 + - - +
23A ASN* 4.0 3.1 - - - +
24A GLU 3.1 29.8 - - - +
25A PRO 5.1 2.5 - - - +
27A LEU* 3.6 19.8 - - - +
30A ARG* 3.9 9.1 - - - +
32A TYR 5.0 0.2 + - - -
93A SER* 3.1 23.4 + - - +
94A TRP* 3.2 61.9 - - + +
95A THR 3.3 21.0 + - - -
120A ALA* 3.6 10.2 - - - +
121A ALA* 1.3 80.7 - - - +
123A LEU* 1.3 62.9 + - - +
147A ILE* 5.4 0.9 - - - -
181A LEU* 4.5 7.4 - - + -
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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