Contacts of the strand formed by residues 117 - 127 (chain B) in PDB entry 5MJ0
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 ASN 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B THR* 3.4 26.2 - - + +
109B LEU 3.2 16.8 - - - +
110B GLN* 4.2 14.4 + - - +
111B ASP 4.6 0.7 - - - +
116B ARG* 1.3 80.0 - - - +
118B LEU* 1.3 73.7 + - - +
119B SER* 4.6 2.9 + - - -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 3.7 17.2 - - + +
38B PRO* 4.5 22.9 - - + +
39B TRP* 4.5 5.2 - - - -
40B ASP* 5.3 3.1 - - - +
45B TYR* 3.6 29.2 - - + +
108B THR* 3.8 0.2 - - - -
109B LEU* 2.9 35.2 + - + +
116B ARG* 4.7 18.2 - - + -
117B ASN* 1.3 84.5 - - - +
119B SER* 1.3 61.2 + - - +
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 3.7 11.1 - - - +
38B PRO* 4.7 5.6 - - - +
106B ARG* 4.3 14.2 - - - -
107B CYS 3.2 10.5 - - - -
108B THR* 2.9 34.7 + - - +
117B ASN* 4.6 3.6 + - - -
118B LEU* 1.3 74.2 - - - +
120B GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B THR* 3.2 20.9 - - - -
37B ALA* 3.9 8.2 - - - +
38B PRO* 5.9 0.2 - - - -
106B ARG* 3.7 4.5 - - - +
107B CYS* 3.0 37.1 + - - +
119B SER* 1.3 75.7 - - - +
121B LYS* 1.3 60.1 + - - -
122B VAL* 4.9 0.9 - - - +
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Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 3.3 40.3 - - - +
21B PRO* 3.6 14.7 - - - +
36B THR* 3.0 13.1 + - - -
52B LEU* 4.2 15.0 - - + +
104B THR* 3.9 26.5 + - + +
105B TYR 3.2 12.6 - - - +
106B ARG* 4.3 7.9 - - + +
120B GLY* 1.3 73.2 - - - -
122B VAL* 1.3 65.6 + - - +
123B ILE* 5.5 4.3 - - - +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 4.3 1.6 - - - -
21B PRO* 3.6 28.3 - - + +
23B VAL* 4.2 22.4 - - + -
33B LEU* 4.4 11.4 - - + -
34B PRO* 3.3 32.8 - - + +
36B THR* 3.5 11.0 - - + +
49B TRP* 4.4 12.1 - - + -
104B THR* 3.5 1.1 - - - -
105B TYR* 2.6 47.7 + - + +
120B GLY 4.9 0.7 - - - +
121B LYS* 1.3 80.0 - - - +
123B ILE* 1.3 66.7 + - - +
124B LEU 4.1 0.2 + - - -
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 4.6 17.5 - - + +
21B PRO 3.0 8.8 + - - +
22B GLU* 3.5 41.2 - - + +
23B VAL* 2.6 37.4 + - - +
33B LEU* 5.2 1.1 - - - -
103B GLY 3.5 8.7 - - - +
104B THR* 3.5 24.7 - - + +
121B LYS* 5.5 3.6 - - - +
122B VAL* 1.3 76.3 - - - +
124B LEU* 1.3 59.7 + - - +
125B ARG* 4.0 26.7 - - + +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 3.5 26.7 - - + +
25B VAL* 4.3 12.3 - - + -
31B VAL* 4.3 16.6 - - + -
33B LEU* 4.4 8.7 - - + -
94B ILE* 4.3 20.6 - - + -
97B THR* 4.6 2.5 - - + -
101B ASN* 3.8 29.8 - - + +
102B SER* 3.1 3.6 - - - -
103B GLY 2.8 33.5 + - - +
105B TYR* 4.0 17.5 - - + -
122B VAL 4.1 1.0 + - - -
123B ILE* 1.3 75.1 - - - +
125B ARG* 1.3 80.7 + - - +
126B VAL* 4.1 11.0 - - + -
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLU* 3.8 26.2 + - - -
23B VAL 2.7 14.7 + - - +
24B LYS* 3.4 38.4 - - + +
25B VAL 2.9 27.5 + - - +
102B SER* 3.8 5.2 - - - -
123B ILE* 4.0 14.2 - - + +
124B LEU* 1.3 80.7 - - - +
126B VAL* 1.3 63.9 + - - +
127B THR* 3.8 6.2 + - + +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B VAL* 3.4 4.7 - - + +
27B SER* 3.6 30.5 - - - +
97B THR* 3.8 18.4 - - + +
98B THR* 3.2 38.1 - - - +
99B SER* 3.8 13.1 + - - +
101B ASN* 4.0 11.7 - - + -
102B SER* 2.8 21.9 + - - +
124B LEU* 4.1 12.8 - - + -
125B ARG* 1.3 74.7 - - - +
127B THR* 1.3 63.0 + - - +
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS* 4.7 21.0 - - + +
25B VAL 2.8 21.2 + - - -
26B ALA* 3.3 7.3 + - - +
27B SER* 2.7 34.8 + - - -
125B ARG* 4.3 12.1 - - + +
126B VAL* 1.3 77.8 - - - +
128B GLY* 1.3 59.0 + - - +
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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