Contacts of the strand formed by residues 118 - 127 (chain F) in PDB entry 4QAE
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 HIS 118 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F TRP* 3.6 5.5 - - - -
112F SER* 4.4 16.5 + - - -
113F THR* 2.6 35.3 + - - -
114F ASN* 3.0 53.3 + - + +
117F GLN* 1.3 89.2 - - - +
119F ALA* 1.3 64.7 + - - +
120F MET* 5.1 2.0 + - - +
137F LEU* 5.0 3.6 - - + +
138F TYR 3.2 11.0 - - - +
144F LEU* 3.9 7.0 - - + -
148F LEU* 3.6 43.4 - - + +
151F ASN* 6.4 0.2 - - - -
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Residues in contact with ALA 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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27F PHE* 3.7 20.4 - - + -
31F TRP* 4.0 2.9 - - + -
112F SER 3.0 12.8 - - - +
113F THR* 3.6 11.7 - - - +
118F HIS* 1.3 82.1 - - - +
120F MET* 1.3 63.5 + - - +
121F VAL* 4.2 1.8 - - + -
137F LEU* 3.4 10.1 - - - +
138F TYR* 2.8 51.1 + - + -
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Residues in contact with MET 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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110F VAL* 3.8 0.3 - - - +
111F VAL* 2.8 35.5 + - + +
112F SER* 2.8 33.2 + - - +
118F HIS* 5.7 2.2 - - - +
119F ALA* 1.3 77.7 - - - +
121F VAL* 1.3 65.1 + - - +
135F VAL* 4.4 6.5 - - + -
136F THR 3.2 7.9 - - - +
137F LEU* 3.8 15.0 - - + -
151F ASN* 3.7 22.7 - - - +
152F PHE* 3.7 39.3 - - + -
155F PHE* 4.0 28.9 - - + -
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Residues in contact with VAL 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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27F PHE* 3.8 17.3 - - + -
56F TYR* 4.5 3.1 - - - +
108F VAL* 3.7 18.2 - - + -
109F ARG 3.4 13.2 - - - +
110F VAL* 4.4 7.6 - - + -
111F VAL* 4.7 0.4 - - - -
119F ALA* 4.4 2.2 - - + -
120F MET* 1.3 80.7 - - - +
122F PHE* 1.3 60.5 + - - +
123F PHE* 3.4 27.2 - - + -
135F VAL* 3.2 9.5 - - - +
136F THR* 2.9 39.9 + - - +
138F TYR* 3.6 30.1 - - + -
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Residues in contact with PHE 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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11F PRO* 4.0 17.3 - - + -
13F LEU* 4.2 18.8 - - + -
16F VAL* 3.5 46.4 - - + -
107F LEU* 4.8 6.5 - - + -
108F VAL* 3.4 4.7 - - - -
109F ARG* 2.9 45.1 + - + +
111F VAL* 4.0 5.3 - - + +
121F VAL* 1.3 73.6 - - - +
123F PHE* 1.3 63.7 + - - +
124F LYS* 3.7 33.9 - - + -
133F PHE* 3.7 29.8 - + + -
134F TRP 3.6 3.8 - - - -
135F VAL* 4.2 11.0 - - + +
155F PHE* 5.2 0.4 - - + -
159F LEU* 3.9 12.6 - - + -
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Residues in contact with PHE 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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52F TRP* 6.4 0.7 - + - -
54F THR* 6.1 0.4 - - + -
56F TYR* 3.8 1.3 - - - -
81F GLN* 6.0 0.7 - - - -
83F PHE* 3.9 25.8 - + - -
94F LEU* 6.1 0.4 - - + -
107F LEU 3.3 6.1 - - - +
108F VAL* 3.8 26.0 - - + -
121F VAL* 3.4 26.7 - - + -
122F PHE* 1.3 77.7 - - - +
124F LYS* 1.3 60.3 + - - +
125F VAL* 6.0 0.2 - - + -
133F PHE* 3.1 8.4 - - - +
134F TRP* 2.9 77.0 + + + +
136F THR* 3.5 30.3 - - + -
138F TYR* 3.4 18.8 - - - -
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Residues in contact with LYS 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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10F ALA* 3.8 19.8 - - + +
11F PRO 5.5 1.4 + - - -
13F LEU* 4.3 22.9 - - + +
106F GLY* 3.2 3.6 - - - -
107F LEU* 2.9 53.2 + - + +
122F PHE* 3.7 19.7 - - + -
123F PHE* 1.3 76.2 - - - +
125F VAL* 1.3 77.6 + - - +
126F VAL* 5.7 4.0 - - - -
131F GLU* 2.9 33.7 + - + +
132F VAL 3.2 11.2 - - - +
133F PHE* 4.2 4.3 - - + -
134F TRP* 4.9 0.2 - - - -
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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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94F LEU* 4.2 20.4 - - + -
105F SER 3.3 13.7 - - - +
106F GLY* 4.2 0.7 - - - -
123F PHE* 6.0 0.4 - - + -
124F LYS* 1.3 84.6 - - - +
126F VAL* 1.3 63.6 + - - +
127F TRP* 4.4 2.2 - - + -
131F GLU* 3.4 4.9 - - - -
132F VAL* 2.8 41.1 + - + +
134F TRP* 4.0 17.3 - - + -
8U ILE* 3.8 15.7 - - + -
9U PHE 4.2 6.5 - - - +
10U CYS* 4.0 4.9 - - - -
13U CYS* 3.6 31.6 - - - -
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Residues in contact with VAL 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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104F THR* 3.6 39.3 + - - +
105F SER* 3.1 29.8 + - - +
124F LYS* 5.7 3.4 - - - -
125F VAL* 1.3 73.6 - - - +
127F TRP* 1.3 60.3 + - - +
128F GLN 4.3 0.8 + - - +
129F ASN* 4.8 15.3 - - - +
130F ARG 3.5 7.6 - - - +
131F GLU* 4.6 18.6 - - + +
8U ILE* 4.3 2.6 - - - +
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Residues in contact with TRP 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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78E TYR* 5.0 0.2 - - - -
175E CYS 6.1 0.4 - - - -
177E ASP 5.4 1.1 - - - -
104F THR* 5.3 6.5 - - + -
125F VAL* 3.7 2.9 + - + -
126F VAL* 1.3 74.5 - - - +
128F GLN* 1.3 105.0 + - + +
129F ASN 3.1 0.9 - - - -
130F ARG* 2.8 55.9 + - - +
132F VAL* 4.2 7.4 - - + -
8U ILE* 3.9 18.4 - - + -
13U CYS* 3.5 43.5 + - + -
14U CYS* 4.0 19.3 - - + +
22U CYS* 3.6 24.9 - - + -
23U CYS 3.3 35.7 - - - -
24U LYS* 3.9 12.8 - - + -
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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