Contacts of the strand formed by residues 118 - 129 (chain F) in PDB entry 3DOY
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 ARG 118 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ASN* 5.4 1.6 - - - +
34F THR* 4.2 9.7 - - - +
45F TYR* 3.3 55.0 - - + -
47F ASN* 3.8 13.2 - - - +
116F GLY 4.0 0.8 + - - +
117F ASP* 1.3 73.1 - - - +
119F LEU* 1.3 58.4 + - - +
120F GLU* 3.3 40.7 + - - +
140F GLN 3.3 13.2 - - - +
141F VAL* 3.8 14.2 - - - +
142F ASP 4.6 3.6 + - - +
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Residues in contact with LEU 119 (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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45F TYR* 3.0 4.2 - - - -
46F LYS* 2.8 45.2 + - + +
48F ILE* 4.2 12.8 - - + -
65F PHE* 4.1 17.9 - - + -
70F ILE* 4.1 22.2 - - + -
113F VAL* 3.8 26.5 - - + -
117F ASP 3.7 1.8 - - - -
118F ARG* 1.3 69.7 - - - +
120F GLU* 1.3 59.6 + - - +
121F TYR* 3.7 33.6 + - + +
139F ALA* 4.1 11.4 - - + -
140F GLN 4.2 0.9 - - - +
141F VAL* 4.0 11.4 - - + -
146F VAL* 4.0 12.1 - - + -
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Residues in contact with GLU 120 (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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34F THR* 4.9 1.9 + - - -
43F VAL* 3.9 14.4 - - + +
44F ALA 3.3 12.3 - - - +
45F TYR* 3.7 2.5 - - + -
118F ARG* 3.3 35.2 + - - +
119F LEU* 1.3 72.6 - - - +
121F TYR* 1.3 62.5 - - - +
122F HIS* 2.7 35.7 + - + +
138F THR 3.9 0.2 - - - +
139F ALA* 3.2 4.7 - - - -
140F GLN* 2.6 56.1 + - - +
143F GLY* 5.6 2.9 + - - -
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Residues in contact with TYR 121 (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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29F LEU* 3.1 27.4 + - - +
30F VAL* 4.2 3.1 - - + -
42F ILE 3.7 0.5 - - - +
43F VAL* 3.2 7.8 - - - +
44F ALA* 2.4 56.6 + - + +
45F TYR* 4.0 4.5 - - - -
46F LYS* 3.7 22.1 - - + +
65F PHE* 5.0 0.3 - - - -
69F LEU 4.4 2.8 + - - -
70F ILE* 3.6 13.5 - - + -
73F GLY* 3.3 27.5 - - - -
74F MET* 3.4 19.3 - - + -
77F SER* 3.1 27.8 - - - +
119F LEU* 3.7 30.1 - - + +
120F GLU* 1.3 70.6 - - - +
122F HIS* 1.3 62.6 + - - +
123F LEU* 3.7 11.4 - - + -
138F THR 3.8 3.1 - - - -
139F ALA* 4.6 4.0 - - + -
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Residues in contact with HIS 122 (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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35F GLU* 5.6 0.9 - - - -
42F ILE 3.7 3.4 - - - -
43F VAL* 3.6 30.9 - - + +
120F GLU* 2.7 40.1 + - + -
121F TYR* 1.3 76.4 - - - +
123F LEU* 1.3 61.8 + - - +
137F GLY* 3.1 6.4 - - - -
138F THR* 2.8 43.4 + - - +
140F GLN* 3.2 33.6 + - + +
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Residues in contact with LEU 123 (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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41F LYS* 3.2 4.6 - - - +
42F ILE* 2.8 50.6 + - + +
74F MET* 3.5 49.1 - - + +
77F SER* 4.0 5.4 - - - -
78F GLY* 4.4 7.2 - - - +
81F LEU* 5.0 0.9 - - + -
121F TYR* 3.7 17.9 - - + -
122F HIS* 1.3 89.8 - - - +
124F GLU* 1.3 58.2 + - - +
135F VAL* 3.8 29.8 - - + -
136F GLY* 3.7 17.5 - - - +
149F ALA 5.2 0.4 - - - +
151F LEU* 5.0 2.9 - - + -
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Residues in contact with GLU 124 (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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40F GLN 3.3 12.3 - - - +
41F LYS* 4.0 7.6 - - + +
81F LEU* 5.0 0.2 - - - -
122F HIS 4.4 0.2 + - - -
123F LEU* 1.3 76.3 - - - +
125F VAL* 1.3 70.9 + - - +
126F LEU* 4.1 17.4 - - + +
135F VAL* 3.3 8.4 - - - +
136F GLY 3.0 35.8 + - - +
137F GLY* 5.8 0.9 - - - -
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Residues in contact with VAL 125 (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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39F ASN 3.7 33.2 - - - +
40F GLN 2.9 10.7 + - - +
81F LEU* 3.7 20.2 - - + -
124F GLU* 1.3 78.1 - - - +
126F LEU* 1.3 65.8 + - - +
127F LYS* 3.8 13.0 - - - +
128F HIS* 3.9 26.0 - - + -
133F TRP* 3.7 28.7 - - + -
134F GLN 4.1 3.4 - - - +
135F VAL* 4.1 3.6 - - + -
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Residues in contact with LEU 126 (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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124F GLU* 4.1 26.7 - - + +
125F VAL* 1.3 75.7 - - - +
127F LYS* 1.3 67.3 + - + +
134F GLN* 2.8 28.2 + - + +
135F VAL 3.8 18.4 - - - +
136F GLY* 3.8 15.7 - - - +
150F GLU* 4.0 29.6 - - + +
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Residues in contact with LYS 127 (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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125F VAL* 3.6 4.8 - - - +
126F LEU* 1.3 82.5 - - - +
128F HIS* 1.3 71.1 + - - +
129F LYS* 6.0 1.3 - - + -
134F GLN* 2.7 59.1 + - + +
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Residues in contact with HIS 128 (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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39F ASN* 3.7 29.0 + - + +
86F LEU* 5.7 3.0 - - + +
125F VAL* 3.9 17.0 - - + -
127F LYS* 1.3 86.3 - - - +
129F LYS* 1.3 68.3 + - - +
130F GLY 5.2 1.8 + - - -
132F ILE 3.3 7.0 - - - +
133F TRP* 3.4 44.8 + + + -
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Residues in contact with LYS 129 (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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127F LYS* 6.0 1.1 - - + -
128F HIS* 1.3 81.0 - - - +
130F GLY* 1.3 69.7 + - - +
131F MET 3.3 0.3 + - - -
132F ILE* 2.9 30.7 + - + +
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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