Contacts of the strand formed by residues 103 - 109 (chain G) in PDB entry 6AHU
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 SER 103 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82F GLU* 3.7 14.7 + - - +
85F LYS* 5.6 3.4 - - - +
101G ASN 4.2 0.4 + - - -
102G THR* 1.3 75.9 - - - +
104G THR* 1.3 77.0 + - - +
105G VAL* 4.2 1.5 - - - +
128G SER* 4.0 5.5 - - - -
129G ALA* 3.5 28.4 + - - +
131G HIS* 4.6 18.6 - - - -
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Residues in contact with THR 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A C 4.2 7.0 - - - +
82F GLU* 2.4 36.2 + - - +
85F LYS* 4.1 6.7 + - - +
86F ARG* 5.4 6.0 - - - -
103G SER* 1.3 82.6 + - - +
105G VAL* 1.3 65.7 + - - +
106G GLU* 4.0 16.7 + - - +
126G ASN* 3.9 31.2 - - + +
127G ASN 3.9 2.5 - - - -
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Residues in contact with VAL 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A A 3.4 34.1 - - - +
21G THR* 3.9 14.4 - - + -
22G LEU 3.9 8.3 - - - +
74G LEU* 4.0 10.1 - - + -
103G SER* 5.4 1.8 - - - +
104G THR* 1.3 77.0 - - - +
106G GLU* 1.3 74.5 + - - +
107G LEU* 4.5 0.4 - - + +
126G ASN* 3.4 2.3 - - - -
127G ASN* 2.9 39.9 + - + +
129G ALA* 3.8 28.5 - - + -
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Residues in contact with GLU 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B GLU* 4.7 6.1 - - - +
533B ASN* 5.9 1.3 - - - +
537B ARG* 3.0 37.2 + - - +
540B LEU* 5.8 6.1 - - + -
21G THR* 4.1 11.3 - - - -
22G LEU* 4.6 2.8 + - + +
104G THR* 4.0 18.6 + - + +
105G VAL* 1.3 87.9 - - - +
107G LEU* 1.3 58.4 + - - +
108G VAL* 4.3 6.1 - - + -
124G ILE* 3.5 28.0 - - + +
125G ARG 3.8 6.9 - - - +
126G ASN* 4.5 6.2 + - - +
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Residues in contact with LEU 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A C 3.3 27.8 - - + +
498B GLU* 4.7 1.3 - - - -
18G VAL* 4.6 4.9 - - + -
20G TYR 4.9 0.9 - - - +
21G THR* 3.8 21.8 - - + -
105G VAL 4.5 2.2 - - - +
106G GLU* 1.3 77.4 + - - +
108G VAL* 1.3 64.3 + - - +
109G ASP* 3.3 38.7 + - - +
124G ILE* 4.1 1.3 - - - +
125G ARG* 2.8 64.3 + - - +
126G ASN* 4.7 0.2 - - - -
127G ASN* 4.3 23.3 - - + +
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Residues in contact with VAL 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B GLU* 3.3 28.5 + - + +
500B PRO* 6.5 0.7 - - + -
537B ARG* 6.4 0.7 - - + -
540B LEU* 3.5 37.9 - - + +
541B LEU* 3.8 29.4 - - + -
18G VAL* 5.0 0.7 - - - +
19G GLU* 4.1 25.8 + - + +
20G TYR 4.6 5.3 + - - +
106G GLU* 5.5 3.4 - - + -
107G LEU* 1.3 75.8 - - - +
109G ASP* 1.3 74.2 + - - +
110G GLU* 4.2 1.5 + - + -
122G THR* 4.8 7.0 - - + -
123G ARG 4.0 4.3 - - - +
124G ILE* 5.1 3.4 - - + -
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Residues in contact with ASP 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A A 5.0 5.9 + - - -
16G ASP* 4.7 10.3 - - - +
17G PRO 4.8 1.6 - - - +
18G VAL* 3.4 32.7 - - - +
107G LEU* 3.3 30.9 + - - +
108G VAL* 1.3 74.8 - - - +
110G GLU* 1.3 59.5 + - - +
111G LEU* 5.9 3.1 - - + -
121G LEU 4.2 0.5 - - - +
122G THR* 3.4 9.5 - - - -
123G ARG* 3.2 44.7 + - + +
125G ARG* 3.6 20.2 + - + +
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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