Contacts of the strand formed by residues 106 - 111 (chain A) in PDB entry 3M8D
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A THR* 5.2 3.0 + - - -
8A LEU* 2.6 35.6 + - - +
28A VAL* 3.8 23.7 - - + +
29A VAL 3.2 13.7 - - - +
30A THR* 4.5 13.1 - - - +
34A ILE* 5.6 0.4 - - - -
104A VAL* 3.7 2.9 - - - +
105A GLN* 1.3 82.9 - - - +
107A VAL* 1.3 75.9 + - - +
108A GLU* 2.8 22.9 + - - -
129A ILE* 3.8 0.3 - - - -
130A ILE* 2.8 54.3 + - + +
132A THR 5.7 0.9 - - - +
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Residues in contact with VAL 107 (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 THR 3.8 0.3 - - - +
28A VAL* 3.4 6.8 - - - +
29A VAL* 2.9 47.8 + - + +
42A VAL* 5.9 2.9 - - + -
45A VAL* 4.4 17.7 - - + -
46A LEU* 4.2 14.1 - - + -
49A LEU* 5.1 0.4 - - + -
104A VAL* 3.7 21.5 - - + -
106A ARG* 1.3 79.0 - - - +
108A GLU* 1.3 70.4 + - - +
109A TYR* 4.5 5.8 - - + -
127A VAL* 4.0 23.8 - - + -
128A ASN 3.4 9.2 - - - +
129A ILE* 4.6 10.1 - - + -
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Residues in contact with GLU 108 (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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9A VAL* 3.5 19.7 - - + +
10A CYS* 3.0 22.6 + - - -
11A THR* 2.5 40.6 + - - +
26A THR* 5.9 0.7 - - + -
27A THR 3.6 4.5 - - - +
28A VAL* 4.5 7.2 - - + -
106A ARG* 2.8 37.8 + - - +
107A VAL* 1.3 76.4 - - - +
109A TYR* 1.3 61.9 + - - +
110A ILE* 4.2 2.2 + - + -
126A VAL 3.7 1.7 - - - +
128A ASN* 2.8 40.7 + - - +
130A ILE* 4.0 15.4 - - + +
708A MTN 3.7 1.4 - - - -
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Residues in contact with TYR 109 (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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26A THR* 3.3 4.7 - - - +
27A THR* 2.9 51.1 + - - +
49A LEU* 3.9 20.2 - - + -
50A PRO 2.8 28.9 + - - -
51A GLY 3.8 1.4 - - - -
52A VAL* 3.2 25.2 - - + +
68A ILE* 3.3 31.1 - - + +
107A VAL* 4.5 11.9 - - + -
108A GLU* 1.3 75.2 - - - +
110A ILE* 1.3 69.1 + - - +
111A ARG* 3.1 42.0 + - + +
126A VAL 3.3 12.8 - - - -
127A VAL* 3.7 15.0 - - + -
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Residues in contact with ILE 110 (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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9A VAL* 5.3 4.0 - - + -
11A THR* 3.7 19.5 - - + -
12A ALA* 3.4 45.1 - - + +
22A VAL* 4.7 1.8 - - + -
24A ALA* 3.8 9.9 - - + -
25A PRO 3.6 9.6 - - - +
26A THR* 4.0 21.8 - - + +
108A GLU* 5.0 0.9 - - + -
109A TYR* 1.3 83.5 - - - +
111A ARG* 1.3 65.6 + - - +
112A GLY 4.4 0.5 - - - +
114A ARG* 3.4 32.5 + - - +
125A GLY* 3.2 2.8 - - - -
126A VAL* 2.8 41.1 + - + +
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Residues in contact with ARG 111 (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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24A ALA* 3.5 24.3 - - - +
25A PRO* 3.0 34.2 + - + +
26A THR 3.7 6.9 + - - +
27A THR* 2.7 32.9 + - - +
50A PRO* 3.2 21.5 + - - +
51A GLY* 4.7 1.6 - - - -
68A ILE* 4.7 3.4 - - + -
69A ARG* 4.0 24.0 - - - +
109A TYR* 3.1 55.9 + - + +
110A ILE* 1.3 73.4 - - - +
112A GLY* 1.3 64.6 + - - +
114A ARG* 4.8 0.3 + - - -
124A GLY 3.9 4.0 - - - +
465A GLU* 2.7 42.7 + - - -
467A THR* 5.3 0.6 - - - +
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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