Contacts of the strand formed by residues 117 - 126 (chain C) in PDB entry 4FQX
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 ASN 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C THR* 3.9 14.0 - - - +
108C LEU 3.6 3.8 + - - -
109C LYS* 3.0 51.4 + - - +
110C PRO 3.3 15.4 + - - -
111C LEU* 4.2 5.3 - - - +
112C GLU 4.6 1.6 + - - +
115C LYS* 4.3 1.2 + - - +
116C PRO* 1.3 77.8 + - - +
118C THR* 1.3 74.3 + - - +
165C ASP* 3.6 3.6 - - - +
166C PHE* 2.8 47.2 + - + +
168C PRO* 3.9 13.6 - - + +
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Residues in contact with THR 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C THR* 3.4 1.9 - - - -
108C LEU* 2.8 56.3 + - + +
109C LYS* 5.4 3.1 + - - -
117C ASN* 1.3 83.9 + - - +
119C LEU* 1.3 73.1 + - - +
120C VAL* 3.6 0.7 + - - +
163C TYR* 3.8 15.5 - - + -
164C LEU 3.3 22.4 - - - +
165C ASP* 2.8 24.6 + - - +
166C PHE* 4.0 4.0 - - - -
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C VAL* 4.3 7.2 - - + -
106C PHE 3.7 0.7 - - - -
107C THR* 3.6 17.7 - - + +
118C THR* 1.3 73.9 - - - +
120C VAL* 1.3 60.7 + - - +
135C TRP* 3.6 24.8 - - + -
163C TYR* 3.4 6.1 - - - -
164C LEU* 2.8 38.0 + - + +
166C PHE* 3.6 31.6 - - + -
174C PHE* 3.5 51.6 - - + -
191C TRP* 3.8 23.1 - - + +
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Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLU 3.3 1.9 - - - +
105C VAL* 3.2 5.9 - - - -
106C PHE* 2.8 67.9 + - + +
108C LEU* 3.8 30.5 - - + +
118C THR 4.1 4.3 - - - +
119C LEU* 1.3 77.6 - - - +
121C CYS* 1.3 63.2 + - - +
122C PHE 3.7 0.4 + - - +
135C TRP* 3.8 2.9 - - - -
161C PHE* 3.9 14.6 - - + -
162C SER 3.6 3.4 - - - +
163C TYR* 3.8 18.6 - - + -
151D ASN 3.9 15.5 - - - +
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Residues in contact with CYS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ALA* 3.9 22.0 - - - -
104C GLU 3.3 5.4 - - - -
105C VAL* 4.5 0.4 - - - -
120C VAL* 1.3 72.3 - - - +
122C PHE* 1.3 61.6 + - - +
123C VAL* 3.7 14.1 + - - +
133C VAL* 4.7 2.2 - - - -
135C TRP* 3.4 20.1 - - + -
161C PHE* 3.4 5.5 - - - -
162C SER* 3.0 34.1 + - - +
176C CYS* 2.0 48.2 - - + -
178C VAL* 4.3 0.4 - - - -
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Residues in contact with PHE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ILE 3.4 3.8 - - - +
103C ALA* 4.4 0.2 - - - -
104C GLU* 2.9 68.7 + - + +
106C PHE* 3.9 20.4 - - + -
120C VAL 3.7 1.2 + - - -
121C CYS* 1.3 71.3 - - - +
123C VAL* 1.3 71.2 + - - +
124C SER* 3.8 19.3 - - - -
159C GLN* 3.2 29.4 - - + -
160C ALA 3.7 2.2 - - - -
161C PHE* 3.4 35.4 - + + -
149D GLN* 3.6 23.3 - - - -
150D PRO* 5.6 5.6 - - + -
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PRO* 4.0 23.6 - - + -
102C ILE 3.2 9.2 - - - +
103C ALA* 4.8 0.2 - - + -
121C CYS* 4.2 13.0 - - - +
122C PHE* 1.3 77.3 - - - +
124C SER* 1.3 63.7 + - - +
126C LEU* 4.7 7.6 - - + -
131C LEU* 4.1 18.6 - - + -
133C VAL* 4.3 7.2 - - + -
159C GLN* 3.4 7.2 - - - +
160C ALA* 2.8 42.4 + - + +
161C PHE* 5.7 0.2 - - - -
162C SER 6.0 0.2 - - - +
178C VAL* 3.7 35.7 - - + -
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Residues in contact with SER 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU* 4.2 8.7 + - - -
101C PRO* 3.3 4.0 - - - +
102C ILE* 2.8 40.9 + - - +
104C GLU* 3.4 16.6 + - - -
122C PHE* 3.8 22.3 + - - -
123C VAL* 1.3 75.8 - - - +
125C ASN* 1.3 69.4 + - - +
126C LEU* 3.2 3.8 + - - +
158C PHE 4.5 3.8 - - - -
159C GLN* 4.6 2.2 - - - -
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Residues in contact with ASN 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TRP* 2.9 35.8 + - - +
44A ARG 5.4 2.8 + - - -
45A LEU* 5.1 0.8 - - - +
46A GLU* 3.2 46.5 + - + +
99C GLY* 4.1 4.6 - - - -
100C PHE 2.9 33.6 + - - +
101C PRO* 3.6 11.7 - - + +
102C ILE* 4.7 12.7 - - + +
124C SER* 1.3 80.5 - - - +
126C LEU* 1.3 61.7 + - - +
127C PHE* 3.7 3.1 + - - -
157C SER* 4.3 3.8 + - - -
158C PHE 3.9 3.2 + - - -
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Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PRO* 4.3 13.5 - - + -
123C VAL* 4.7 5.8 - - + -
124C SER 4.2 5.8 - - - +
125C ASN* 1.3 74.2 - - - +
127C PHE* 1.3 63.1 + - - +
128C PRO 3.6 20.0 - - - +
129C PRO* 4.1 12.8 - - + -
130C MET 4.3 0.7 - - - +
131C LEU* 3.9 44.2 - - + -
150C VAL* 4.6 3.8 - - + -
157C SER* 3.5 0.9 + - - -
158C PHE* 2.9 53.0 + - + +
159C GLN* 4.5 4.0 - - - +
160C ALA* 4.3 13.7 - - + -
180C HIS* 3.6 20.6 - - + -
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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