Contacts of the strand formed by residues 113 - 122 (chain D) 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 VAL 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D LYS* 3.9 34.5 - - + +
106D PRO* 4.5 2.5 - - - -
109D THR* 5.5 0.2 - - - +
111D GLU* 3.3 3.4 - - - +
112D PRO* 1.3 87.3 - - + +
114D MET* 1.3 63.8 + - - +
115D LEU* 4.0 17.0 - - + -
162D LEU 4.1 0.2 - - - +
163D ALA* 3.5 5.5 - - - +
164D LEU* 3.2 50.1 + - + +
166D PRO* 3.8 27.8 - - + -
189D TRP* 4.2 5.8 - - + -
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Residues in contact with MET 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LYS* 3.4 5.1 - - - +
104D THR* 2.9 50.6 + - + +
106D PRO* 3.8 22.4 - - + +
107D PHE* 3.9 40.6 - - + +
109D THR* 4.7 2.5 - - + -
113D VAL* 1.3 76.5 - - - +
115D LEU* 1.3 68.1 + - - +
141D HIS* 3.5 24.9 - - + -
161D HIS* 3.6 9.0 - - + +
162D LEU 3.5 7.6 - - - -
163D ALA* 3.2 42.4 - - + +
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D VAL* 4.1 4.9 - - + -
102D ALA 3.4 5.2 - - - +
103D LYS* 4.1 7.9 - - + -
113D VAL* 4.0 10.5 - - + -
114D MET* 1.3 76.1 - - - +
116D ALA* 1.3 60.6 + - - +
117D CYS 4.2 0.2 - - - -
131D TRP* 3.9 27.0 - - + -
161D HIS* 3.2 8.8 + - - +
162D LEU* 3.1 29.4 + - + +
164D LEU* 3.7 25.8 - - + -
172D TYR* 3.9 15.5 - - + -
189D TRP* 3.5 61.2 - - + +
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Residues in contact with ALA 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLN 3.6 0.3 - - - +
101D VAL* 3.4 3.9 - - - -
102D ALA 2.8 31.3 + - - +
104D THR* 3.9 14.1 - - + +
115D LEU* 1.3 75.3 - - - +
117D CYS* 1.3 62.2 + - - +
118D TYR* 3.6 30.7 + - + +
131D TRP* 4.4 2.5 - - - -
159D LEU* 5.1 2.2 - - + -
160D SER 3.4 4.3 - - - -
161D HIS* 3.9 20.6 - - + +
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Residues in contact with CYS 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL* 4.6 3.1 - - - -
100D GLN 3.5 4.7 - - - -
101D VAL* 4.1 4.9 - - + -
116D ALA* 1.3 71.0 - - - +
118D TYR* 1.3 63.1 + - - +
119D VAL* 3.8 21.7 + - - +
129D ILE* 4.4 3.8 - - - -
131D TRP* 3.6 18.2 - - + -
159D LEU* 3.2 25.0 - - - -
160D SER* 2.8 16.8 + - - +
174D CYS* 2.0 45.3 - - + -
176D VAL* 4.0 3.4 - - - -
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Residues in contact with TYR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C PRO* 3.7 31.6 - - + -
111C LEU 6.0 0.4 - - - -
194C ARG 5.4 0.2 + - - -
195C ASN* 3.7 26.7 + - - +
197C LEU* 3.6 35.6 - - + +
98D SER 3.9 0.2 - - - +
99D VAL* 3.2 8.0 - - - +
100D GLN* 2.9 34.0 + - + +
102D ALA* 4.5 8.3 - - + -
103D LYS 4.9 2.1 + - - -
104D THR* 4.3 4.9 + - - -
116D ALA* 3.7 30.0 - - + +
117D CYS* 1.3 72.7 - - - +
119D VAL* 1.3 61.8 + - - +
120D TRP* 4.0 4.7 - - + -
158D THR 3.9 4.5 - - - +
159D LEU* 4.4 23.6 - - + -
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Residues in contact with VAL 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D PRO* 3.7 16.4 - - + -
98D SER 3.6 2.5 - - - -
99D VAL* 4.1 3.4 - - + -
117D CYS* 3.8 7.2 - - - +
118D TYR* 1.3 80.7 - - - +
120D TRP* 1.3 63.4 + - - +
122D PHE* 3.1 28.2 - - + -
127D VAL* 4.4 3.8 - - + -
129D ILE* 3.8 19.5 - - + -
157D GLN* 3.2 1.2 - - - +
158D THR* 2.7 50.5 + - + +
176D VAL* 3.8 36.1 - - + -
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Residues in contact with TRP 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU 4.1 17.7 - - - +
109C LYS* 4.3 17.6 - - + +
110C PRO* 3.3 42.9 - - + +
97D PRO* 3.4 2.3 - - - +
98D SER* 3.0 76.8 + - - -
99D VAL 4.4 0.2 - - - -
100D GLN* 3.6 38.8 - - + -
118D TYR* 4.0 8.5 - - + -
119D VAL* 1.3 78.0 - - - +
121D GLY* 1.3 64.7 + - - +
122D PHE* 3.1 12.3 + - - -
156D TYR 3.6 5.4 - - - -
157D GLN* 3.9 13.7 - - + -
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Residues in contact with GLY 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ARG* 3.4 18.7 - - - +
96D PRO 4.0 5.3 - - - +
120D TRP* 1.3 83.7 - - - +
122D PHE* 1.3 62.8 + - - +
151D ASN* 4.9 2.6 - - - +
155D THR* 3.7 24.2 - - - +
156D TYR 3.1 7.5 + - - -
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Residues in contact with PHE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ARG 3.2 13.5 - - - +
96D PRO 4.1 0.9 - - - -
97D PRO* 3.6 18.6 - - + -
119D VAL* 3.1 45.8 - - + -
120D TRP 3.1 7.9 + - - -
121D GLY* 1.3 79.8 - - - +
123D TYR* 1.3 59.8 + - - +
124D PRO 3.2 18.6 - - - -
125D ALA 3.1 24.5 - - - -
127D VAL* 4.0 17.7 - - + -
148D ALA* 3.9 12.6 - - + -
155D THR* 3.2 5.9 - - - -
156D TYR* 2.6 58.2 + - + -
157D GLN* 4.0 4.7 - - - -
158D THR* 4.1 2.2 - - + -
178D HIS* 3.7 13.7 - + + -
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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