Contacts of the strand formed by residues 117 - 126 (chain A) in PDB entry 5MIX
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A THR* 3.9 19.1 - - + +
109A LEU 3.2 7.4 - - - +
110A GLN* 2.8 49.7 + - - +
116A ARG* 1.3 80.7 + - - +
118A LEU* 1.3 70.0 + - - +
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Residues in contact with LEU 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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37A ALA* 3.7 15.3 - - + +
38A PRO* 3.4 37.7 - - + +
39A TRP* 4.3 4.3 - - - -
40A ASP 5.3 0.2 - - - +
45A TYR* 3.4 36.8 - - + +
108A THR* 3.3 3.3 - - - -
109A LEU* 2.7 44.1 + - + +
116A ARG* 5.3 7.9 - - + +
117A ASN* 1.3 79.8 - - - +
119A SER* 1.3 61.2 + - - +
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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
----------------------------------------------------------
37A ALA* 3.8 9.7 - - - -
38A PRO* 4.2 6.4 - - - +
106A ARG* 4.3 14.7 - - - -
107A CYS 3.1 13.7 - - - -
108A THR* 3.6 15.3 - - - -
118A LEU* 1.3 77.7 - - - +
120A GLY* 1.3 58.7 + - - +
121A LYS* 5.8 1.4 + - - -
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Residues in contact with GLY 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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36A THR* 3.2 18.4 - - - -
37A ALA* 3.9 12.7 - - - +
49A TRP* 5.6 0.3 - - - -
106A ARG* 3.5 2.9 - - - +
107A CYS* 3.0 33.0 + - - -
119A SER* 1.3 75.8 - - - +
121A LYS* 1.3 64.1 + - - -
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Residues in contact with LYS 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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20A THR* 3.6 27.2 - - + +
21A PRO* 3.8 5.4 - - - +
36A THR* 2.8 18.4 + - - +
52A LEU* 3.7 28.7 - - + -
104A THR* 4.3 9.9 - - + -
105A TYR 3.2 11.9 - - - +
106A ARG* 4.2 16.2 - - + +
119A SER* 5.8 1.4 + - - -
120A GLY* 1.3 77.5 - - - +
122A VAL* 1.3 63.3 + - - +
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Residues in contact with VAL 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 THR* 3.7 4.9 - - - -
21A PRO* 3.7 18.4 - - + +
23A VAL* 4.0 20.6 - - + -
33A LEU* 4.2 13.0 - - + -
34A PRO* 3.8 30.7 - - + +
36A THR* 4.2 2.5 - - + -
49A TRP* 4.0 21.8 - - + -
103A GLY 4.0 0.2 - - - +
104A THR* 3.6 1.3 - - - -
105A TYR* 2.8 38.8 + - + +
121A LYS* 1.3 77.2 - - - +
123A ILE* 1.3 75.2 + - - +
124A LEU 4.0 0.2 + - - -
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Residues in contact with ILE 123 (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 THR* 3.9 26.9 - - + +
21A PRO 2.9 11.7 + - - +
22A GLU* 3.4 35.6 - - + +
23A VAL* 2.8 32.7 + - - +
103A GLY* 3.5 10.3 - - - +
104A THR* 3.8 20.0 - - + +
122A VAL* 1.3 80.5 - - - +
124A LEU* 1.3 65.8 + - - +
125A ARG* 4.1 19.5 - - + +
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Residues in contact with LEU 124 (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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23A VAL* 3.4 20.0 - - + +
25A VAL* 3.8 24.7 - - + -
31A VAL* 4.4 10.3 - - + -
33A LEU* 4.0 21.5 - - + -
94A ILE* 4.1 21.5 - - + -
97A THR* 5.0 0.9 - - + -
101A ASN* 3.5 29.8 - - + +
102A SER* 3.2 3.6 - - - -
103A GLY 2.8 33.1 + - - +
105A TYR* 4.0 15.3 - - + -
122A VAL 4.0 0.6 + - - -
123A ILE* 1.3 75.0 - - - +
125A ARG* 1.3 65.9 + - - +
126A VAL* 4.1 14.4 - - + -
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Residues in contact with ARG 125 (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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22A GLU* 2.7 40.5 + - + +
23A VAL 2.8 11.6 + - - +
24A LYS* 3.2 36.4 - - + +
25A VAL 3.0 24.1 + - - -
102A SER* 3.8 4.5 - - - -
123A ILE* 4.1 17.3 - - + +
124A LEU* 1.3 78.4 - - - +
126A VAL* 1.3 63.3 + - - +
127A THR* 3.9 6.8 + - + -
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Residues in contact with VAL 126 (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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25A VAL* 3.3 20.9 - - + +
27A SER* 3.2 34.7 + - - +
97A THR* 3.9 14.6 - - - +
98A THR 3.3 34.3 - - - +
99A SER* 3.9 9.3 + - - +
101A ASN* 4.1 11.0 - - + -
102A SER* 2.9 23.0 + - - +
124A LEU* 4.1 9.2 - - + -
125A ARG* 1.3 72.1 - - - +
127A THR* 1.3 65.4 + - - +
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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