Contacts of the strand formed by residues 96 - 103 (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 SER 96 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89G PHE* 4.1 2.0 - - - -
94G MET* 3.2 22.0 - - - +
95G ALA* 1.3 81.2 - - - +
97G THR* 1.3 66.4 + - - +
143G ARG* 3.8 26.2 + - - +
144G VAL 3.5 8.0 + - - -
145G ASP* 3.6 11.2 + - - -
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Residues in contact with THR 97 (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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87G VAL* 5.4 0.2 - - + -
89G PHE* 3.4 29.4 - - + -
94G MET* 4.3 8.3 - - - -
96G SER* 1.3 78.6 + - - +
98G THR* 1.3 74.3 + - - +
99G LEU* 3.8 15.7 - - + +
117G SER* 5.4 4.0 + - - -
120G VAL* 4.1 15.1 - - + +
143G ARG* 3.3 12.9 - - - +
144G VAL* 3.0 42.2 + - + -
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Residues in contact with THR 98 (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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97G THR* 1.3 87.5 + - - +
99G LEU* 1.3 63.9 + - - +
100G ILE* 3.9 21.9 + - + +
115G THR 5.6 0.7 - - - +
117G SER* 5.5 6.8 - - - -
141G GLU* 4.9 3.3 + - - +
142G VAL 3.1 16.4 + - - -
143G ARG* 4.3 4.9 - - - +
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Residues in contact with LEU 99 (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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85G LEU* 4.8 7.4 - - + -
87G VAL* 4.9 13.9 - - + -
97G THR* 3.8 13.2 - - + +
98G THR* 1.3 77.6 - - - +
100G ILE* 1.3 65.9 + - - +
114G PHE* 3.6 36.6 - - + -
115G THR 5.1 7.6 - - - +
120G VAL* 5.2 8.7 - - + -
122G ILE* 4.5 17.5 - - + -
141G GLU* 3.2 6.1 - - - -
142G VAL* 2.9 44.5 + - + +
144G VAL* 3.7 26.9 - - + -
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Residues in contact with ILE 100 (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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98G THR* 3.9 16.4 - - + +
99G LEU* 1.3 85.6 - - - +
101G LEU* 1.3 65.4 + - - +
102G ARG* 5.4 4.0 - - + -
114G PHE* 3.3 4.0 - - - -
115G THR* 2.5 60.6 + - + +
139G TYR* 4.3 20.6 - - + +
140G MET 3.8 0.9 - - - -
141G GLU* 3.8 24.9 - - + +
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Residues in contact with LEU 101 (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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100G ILE* 1.3 77.0 - - - +
102G ARG* 1.3 76.6 + - - +
103G ALA* 4.5 2.7 - - + +
109G VAL* 3.6 32.3 - - + -
113G ASP* 3.2 33.7 - - + +
114G PHE* 4.0 22.0 - - + +
115G THR* 4.8 0.7 - - - -
129G ILE* 5.1 4.0 - - + -
138G LEU* 4.9 9.0 - - + +
139G TYR* 3.6 5.5 - - - -
140G MET* 2.9 72.4 + - + +
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Residues in contact with ARG 102 (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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100G ILE* 5.2 4.2 - - + +
101G LEU* 1.3 81.3 - - - +
103G ALA* 1.3 62.2 + - - +
104G GLU* 4.1 21.6 + - - +
107G LYS* 5.3 3.5 + - - -
113G ASP 5.0 2.4 + - - +
115G THR* 5.4 0.6 + - - -
138G LEU 3.6 4.5 - - - -
139G TYR* 3.6 38.1 - - + +
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Residues in contact with ALA 103 (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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101G LEU* 4.2 5.5 - - + +
102G ARG* 1.3 74.8 - - - +
104G GLU* 1.3 62.8 + - - +
107G LYS* 4.3 16.8 - - + +
109G VAL* 3.8 41.1 - - + -
113G ASP* 5.4 0.9 - - + +
132G LEU* 3.3 11.5 - - + +
138G LEU* 2.9 36.7 + - + +
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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