Contacts of the strand formed by residues 10 - 16 (chain G) in PDB entry 4XLN
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 VAL 10 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8G ALA 3.4 6.9 + - - +
9G PRO* 1.3 71.5 - - - +
11G PHE* 1.3 61.9 + - - +
12G THR* 3.9 22.2 - - + -
24G VAL 3.4 3.6 - - - +
25G LEU* 3.5 1.6 - - - -
26G GLU* 2.8 42.0 + - + +
27G PRO* 4.4 0.2 - - - +
186G LEU* 3.7 24.0 - - + -
229H GLU* 4.2 11.9 - - - +
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Residues in contact with PHE 11 (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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9G PRO 3.5 4.2 + - - +
10G VAL* 1.3 74.6 - - - +
12G THR* 1.3 78.8 + - - +
13G ALA* 4.4 3.4 - - + -
23G PHE* 3.8 26.9 - + + -
24G VAL 3.4 8.3 - - - -
25G LEU* 3.6 11.2 - - + -
211G LEU* 5.0 0.9 - - + -
224H TYR 3.4 23.1 - - - +
225H PHE* 3.3 46.9 - + + -
226H ALA 4.0 6.5 - - - -
227H ASN* 3.4 29.6 + - - +
228H PRO* 3.8 27.1 - - + -
229H GLU* 3.5 14.1 + - - +
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Residues in contact with THR 12 (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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10G VAL* 3.9 16.8 - - + -
11G PHE* 1.3 86.1 - - - +
13G ALA* 1.3 61.1 + - - +
14G THR* 5.4 3.1 + - - -
23G PHE* 3.5 4.0 - - - -
24G VAL* 2.9 56.9 + - + +
229H GLU* 3.9 29.8 - - + +
231H SER* 6.1 0.9 - - - -
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Residues in contact with ALA 13 (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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11G PHE* 4.4 1.3 - - + -
12G THR* 1.3 76.5 - - - +
14G THR* 1.3 62.1 + - - +
15G THR* 3.7 4.3 + - - +
22G GLU 3.3 4.3 - - - -
23G PHE* 3.7 26.0 - - + -
208G LEU* 4.8 8.5 - - + -
228H PRO* 3.5 26.9 - - + -
229H GLU 2.8 27.5 + - - +
230H ALA* 3.4 11.6 - - - -
231H SER* 4.8 0.2 - - - -
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Residues in contact with THR 14 (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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12G THR* 4.3 3.4 + - - -
13G ALA* 1.3 69.0 - - - +
15G THR* 1.3 62.2 + - - +
16G GLN* 5.4 0.6 - - + +
20G TYR* 6.0 1.0 - - + -
21G GLY* 3.5 2.1 - - - -
22G GLU* 2.8 57.8 + - + +
24G VAL* 6.0 2.2 - - - +
208G LEU* 5.7 0.7 - - - -
231H SER* 2.7 36.0 + - - +
233H LEU* 3.6 34.1 - - + +
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Residues in contact with THR 15 (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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13G ALA* 3.7 8.5 + - - +
14G THR* 1.3 74.6 - - - +
16G GLN* 1.3 65.6 + - - +
17G GLY 3.7 18.8 - - - +
20G TYR 4.2 4.0 - - - +
21G GLY* 4.7 1.1 - - - -
206G THR* 5.9 1.8 - - - -
207G PRO* 5.5 2.9 - - + -
208G LEU* 3.4 38.2 - - + +
230H ALA* 5.1 5.4 - - - +
231H SER 3.7 4.0 + - - -
232H LEU* 3.1 43.6 - - - +
233H LEU 4.3 0.5 + - - -
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Residues in contact with GLN 16 (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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14G THR* 4.0 1.3 + - + +
15G THR* 1.3 79.8 - - - +
17G GLY* 1.3 65.3 + - - +
19G HIS* 3.6 16.7 + - + +
20G TYR* 2.8 67.9 + - + +
232H LEU* 4.4 12.0 - - - +
233H LEU* 3.6 38.1 - - + +
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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