Contacts of the strand formed by residues 108 - 114 (chain M) in PDB entry 3TDD
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 GLN 108 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7M LYS* 3.9 26.6 + - + +
8M TYR 2.6 26.9 + - - -
9M ASP 3.5 14.8 + - - -
10M ASN 4.6 1.1 - - - -
11M GLY* 3.5 26.2 - - - +
12M VAL* 3.8 14.1 - - + -
14M ILE* 3.6 16.0 + - - +
103M GLY 3.6 4.0 - - - -
104M VAL* 4.5 2.0 - - + +
105M GLN* 5.2 0.9 - - - +
106M GLY 4.6 5.8 - - - +
107M ASP* 1.3 82.6 - - - +
109M PHE* 1.3 61.8 + - - +
110M LEU 4.3 0.2 - - - -
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Residues in contact with PHE 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M LYS* 5.0 0.2 - - - +
12M VAL* 3.9 2.9 - - - +
76M PRO* 4.0 17.9 - - + -
77M SER* 3.7 28.7 - - - -
80M PHE* 3.5 41.7 - + + -
101M VAL* 3.5 29.2 - - + -
102M ALA* 3.5 3.6 - - - -
103M GLY 2.6 40.5 + - - +
105M GLN* 4.3 14.1 - - + +
108M GLN* 1.3 76.4 - - - +
110M LEU* 1.3 64.8 + - - +
111M ARG* 3.7 25.6 - - + -
121M SER* 6.0 0.2 - - - -
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Residues in contact with LEU 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M SER* 3.6 29.4 - - - +
6M MET* 3.9 15.9 - - - -
7M LYS* 3.9 23.1 + - + +
12M VAL* 4.5 8.1 - - + -
100M ILE* 4.0 4.9 - - + -
101M VAL 3.4 3.1 - - - +
102M ALA* 3.6 31.2 - - + -
108M GLN 4.3 0.4 + - - -
109M PHE* 1.3 78.2 - - - +
111M ARG* 1.3 61.1 + - - +
121M SER* 2.8 23.6 + - - -
122M SER 3.8 18.9 + - - +
123M PRO 3.9 14.1 - - - +
125M LEU* 3.6 17.5 - - + +
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Residues in contact with ARG 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L GLU* 3.0 25.3 + - - -
53L ASP* 4.6 5.1 + - - -
80M PHE* 3.3 47.0 - - + -
100M ILE* 3.4 3.6 - - - +
101M VAL 2.9 32.6 + - - +
109M PHE* 3.7 16.5 - - + -
110M LEU* 1.3 75.2 - - - +
112M TYR* 1.3 63.8 + - - +
119M THR* 3.2 27.3 + - - -
120M TYR* 3.4 9.2 - - - +
121M SER* 3.1 37.2 + - - +
125M LEU* 3.7 4.2 - - - +
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Residues in contact with TYR 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M PHE* 3.5 3.0 - - - -
98M ALA* 4.1 9.5 - - + +
99M ILE 3.2 13.9 - - - +
100M ILE* 4.0 7.2 - - + -
111M ARG* 1.3 74.9 - - - +
113M VAL* 1.3 63.0 + - - +
114M ASN* 3.1 47.7 + - + +
118M VAL 3.8 3.8 - - - -
119M THR* 3.0 30.7 - - - +
120M TYR* 3.0 63.4 + + + +
125M LEU* 4.1 10.1 - - + -
126M ALA 4.5 7.4 - - - -
127M THR* 3.6 32.4 - - + -
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Residues in contact with VAL 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M PHE* 4.1 14.4 - - + -
83M LEU* 4.8 3.8 - - + -
84M ALA* 3.8 26.0 - - - +
87M MET* 3.8 19.7 - - + -
99M ILE* 2.7 68.4 + - + +
101M VAL* 5.7 0.2 - - + -
112M TYR* 1.3 79.6 - - - +
114M ASN* 1.3 61.6 + - - +
117M GLY* 4.3 5.4 - - - -
118M VAL 3.1 7.9 - - - +
119M THR* 3.7 19.5 - - + -
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Residues in contact with ASN 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M MET* 3.3 18.7 - - - +
97M ASN 3.2 14.8 - - - +
98M ALA* 4.1 3.4 - - + -
112M TYR* 3.1 35.8 + - + +
113M VAL* 1.3 73.2 - - - +
115M LEU* 1.3 71.1 + - + +
116M LEU* 2.9 22.3 + - - +
117M GLY 2.9 17.0 + - - -
118M VAL* 3.3 26.9 + - - +
120M TYR* 5.6 0.4 - - - -
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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