Contacts of the strand formed by residues 99 - 105 (chain F) in PDB entry 1XWD
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 GLU 99 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D THR* 3.4 24.2 + - - -
88D TYR* 2.6 28.8 + - - +
96E VAL* 5.5 0.2 - - - +
73F GLU 3.0 3.4 + - - -
74F LYS* 3.4 35.5 + - + +
75F ILE 3.0 25.6 + - - +
76F GLU* 5.6 3.1 - - - +
97F LEU* 3.4 8.4 - - - +
98F HIS* 1.3 81.7 - - + +
100F ILE* 1.3 66.5 + - - +
101F ARG* 3.3 31.1 + - - +
124F TYR* 3.3 22.0 - - + +
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Residues in contact with ILE 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ILE* 3.6 7.2 - - + +
77F ILE* 6.1 0.2 - - + -
91F PHE* 3.8 31.2 - - + -
97F LEU* 3.8 17.7 - - + -
99F GLU* 1.3 77.3 - - - +
101F ARG* 1.3 65.8 + - - +
102F ILE* 4.0 21.8 - - + -
116F PHE* 3.6 27.6 - - + -
119F LEU* 4.1 2.5 - - + -
122F LEU* 3.7 22.9 - - + -
124F TYR* 2.8 10.3 + - - +
125F LEU* 4.0 18.6 - - + -
126F LEU* 2.8 27.0 + - - +
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Residues in contact with ARG 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D THR* 4.4 6.1 - - - +
87D CYS 5.6 1.0 + - - -
94E CYS 4.9 2.4 + - - -
95E THR* 4.6 6.1 - - - +
96E VAL* 3.1 47.2 - - - +
97E ARG 4.7 2.4 + - - +
75F ILE 2.8 14.1 + - - +
76F GLU* 4.0 30.2 + - + +
77F ILE* 2.7 33.4 + - - +
78F SER* 5.7 0.2 + - - -
99F GLU* 3.3 31.2 + - - +
100F ILE* 1.3 73.4 - - - +
102F ILE* 1.3 60.1 + - - +
103F GLU* 2.8 29.8 + - + +
124F TYR* 3.9 9.3 + - + -
126F LEU* 3.1 40.3 - - + +
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Residues in contact with ILE 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F ILE* 3.3 25.6 - - + +
83F LEU* 5.6 0.7 - - + -
86F ILE* 4.1 22.2 - - + -
91F PHE* 4.2 10.5 - - + -
100F ILE* 4.0 20.9 - - + -
101F ARG* 1.3 75.9 - - - +
103F GLU* 1.3 63.7 + - - +
105F ALA* 4.5 6.7 - - + -
108F LEU* 4.0 25.6 - - + -
111F ILE* 5.1 2.5 - - + -
116F PHE* 4.7 4.3 - - + -
126F LEU 2.8 12.0 + - - +
127F ILE* 3.2 29.7 - - + -
128F SER 2.8 26.2 + - - +
130F THR* 4.4 4.9 - - - +
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Residues in contact with GLU 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ASP* 4.4 1.6 - - - +
94E CYS 4.1 5.8 - - - +
95E THR* 3.3 26.1 - - - +
76F GLU* 5.4 0.2 - - - +
77F ILE 2.9 11.3 + - - +
78F SER* 3.4 15.2 + - - +
79F GLN 2.8 25.3 + - - -
80F ASN* 4.6 0.9 + - - -
101F ARG* 2.8 44.0 + - + +
102F ILE* 1.3 80.2 - - - +
104F LYS* 1.3 82.0 + - - +
105F ALA* 3.3 3.6 + - - +
126F LEU* 3.9 20.4 - - + -
128F SER* 3.4 14.0 - - - +
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Residues in contact with LYS 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D SER* 5.2 1.3 - - - +
46D THR* 3.2 39.4 - - - +
47D MET* 4.1 15.9 - - + -
93E ASP* 3.3 24.5 + - - +
95E THR* 3.2 28.1 - - - +
97E ARG 5.1 0.2 + - - -
98E GLY* 5.7 0.4 - - - -
78F SER* 3.8 5.1 + - - -
79F GLN* 3.5 36.6 - - + +
80F ASN 3.2 19.2 + - - +
103F GLU* 1.3 99.9 + - - +
105F ALA* 1.3 57.2 + - - +
106F ASN 3.4 0.9 + - - -
128F SER* 3.0 12.2 + - - -
129F ASN* 3.4 24.2 - - + +
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Residues in contact with ALA 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F ILE* 6.1 0.7 - - + -
80F ASN* 3.8 14.4 - - + +
83F LEU* 4.7 11.4 - - + +
102F ILE* 4.5 9.0 - - + -
103F GLU 3.3 1.7 - - - +
104F LYS* 1.3 74.6 - - - +
106F ASN* 1.3 64.5 + - - +
107F ASN 3.1 3.4 - - - -
108F LEU* 3.0 43.5 + - + +
129F ASN 3.1 6.5 + - - -
130F THR* 3.3 23.0 + - - +
131F GLY 3.6 0.2 + - - -
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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