Contacts of the strand formed by residues 110 - 119 (chain I) in PDB entry 4XLQ
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 110 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69I LEU* 3.2 20.4 - - - +
97I ARG* 2.8 27.4 + - - +
98I LEU 3.2 20.4 - - - +
99I GLN* 3.7 17.9 - - + +
108I ILE* 3.0 9.0 + - + +
109I LYS* 1.3 86.1 + - - +
111I ASP* 1.3 66.5 + - - +
369I PRO* 4.6 0.2 - - - -
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Residues in contact with ASP 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ARG* 4.2 6.0 + - - +
98I LEU* 2.8 39.6 + - - +
109I LYS* 5.8 1.1 - - - -
110I GLU* 1.3 78.6 - - - +
112I GLU* 1.3 71.7 + - - +
113I VAL 3.7 0.2 - - - -
368I THR* 3.8 15.5 - - - +
369I PRO* 3.4 23.1 - - + +
370I ALA* 3.5 23.9 - - - +
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Residues in contact with GLU 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I ARG* 4.7 12.5 + - - +
95I TYR* 3.7 31.2 - - - +
96I ALA 3.4 15.5 - - - +
97I ARG* 3.3 45.4 + - + +
111I ASP* 1.3 82.5 + - - +
113I VAL* 1.3 71.8 + - - +
370I ALA* 5.6 0.3 - - - +
295L GLN* 4.5 8.5 - - - +
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Residues in contact with VAL 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I TYR* 4.2 1.0 - - - +
96I ALA* 2.8 43.0 + - + +
98I LEU* 3.5 27.6 - - + -
111I ASP 3.4 2.1 + - - +
112I GLU* 1.3 85.5 - - - +
114I PHE* 1.3 65.9 + - - +
115I LEU* 5.2 1.1 - - + -
369I PRO* 3.4 36.3 - - + +
370I ALA* 3.6 11.4 - - + +
373I VAL* 3.7 24.2 - - + -
295L GLN* 4.5 9.4 - - + +
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Residues in contact with PHE 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I PRO* 3.3 31.4 - - + -
94I LEU 3.7 10.8 - - - -
95I TYR* 3.7 24.0 - + + -
96I ALA 4.2 3.6 - - - +
113I VAL* 1.3 80.2 - - - +
115I LEU* 1.3 67.9 + - - +
116I GLY* 3.1 32.1 - - - -
117I HIS* 3.7 10.1 - + - -
373I VAL* 4.3 7.3 - - - +
374I ASN 4.1 8.7 - - - +
375I SER* 3.8 11.7 + - - -
294L GLN* 3.2 38.4 - - + -
295L GLN* 3.5 36.8 - - + +
298L GLY* 4.0 8.1 - - - -
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Residues in contact with LEU 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I PHE* 4.3 13.7 - - + -
71I TYR* 5.0 0.2 - - + -
94I LEU* 3.3 44.7 + - + +
95I TYR 4.3 0.4 - - - +
96I ALA* 3.6 29.4 - - + -
113I VAL* 5.2 1.1 - - + -
114I PHE* 1.3 80.7 - - - +
116I GLY* 1.3 60.7 + - - +
344I PHE* 4.3 7.2 - - + -
348I LEU* 5.0 8.3 - - + -
351I LEU* 5.4 2.0 - - + -
373I VAL* 5.1 11.2 - - + -
374I ASN 4.8 2.2 - - - -
375I SER* 3.2 35.7 + - - +
378I LEU* 3.5 33.1 - - + +
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Residues in contact with GLY 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I PRO* 3.4 0.3 - - - +
94I LEU* 2.9 25.9 + - - -
114I PHE* 3.1 18.1 - - - -
115I LEU* 1.3 83.1 - - - +
117I HIS* 1.3 66.5 + - - -
378I LEU* 5.8 0.4 - - - -
379I GLU* 3.6 20.2 - - - -
294L GLN* 4.3 0.7 - - - -
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Residues in contact with HIS 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I PRO* 5.0 4.2 - - + +
91I GLN* 3.1 43.3 - - + +
92I ALA 3.5 4.0 - - - +
93I PRO* 3.3 32.3 - - + +
114I PHE* 3.7 22.2 - + - -
116I GLY* 1.3 75.6 - - - -
118I LEU* 1.3 61.0 + - - +
119I PRO* 3.7 5.7 - - - +
379I GLU* 3.0 29.2 + - - +
382I LEU* 5.6 5.1 - - - +
299L ARG* 4.4 14.3 - - - +
300L GLU* 3.7 26.2 + - + +
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Residues in contact with LEU 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I TYR* 4.4 12.3 - - - +
30I LEU* 5.2 4.9 - - + -
44I ILE* 4.5 11.0 - - + -
91I GLN* 3.7 2.7 - - - -
92I ALA* 3.0 30.3 + - - +
94I LEU* 4.6 15.7 - - + -
116I GLY 4.2 0.6 + - - -
117I HIS* 1.3 71.0 - - - +
119I PRO* 1.3 89.5 - - + +
120I LEU* 3.7 4.3 + - - +
340I MET* 4.5 23.3 - - + -
344I PHE* 4.3 18.6 - - + -
382I LEU* 3.6 27.4 - - + -
386I PHE* 4.6 6.7 - - + -
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Residues in contact with PRO 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I TYR* 2.9 21.5 + - - -
89I THR* 3.8 23.3 - - + -
90I TYR 2.9 13.9 - - - +
91I GLN* 3.8 2.7 - - + +
117I HIS 3.7 7.6 - - - +
118I LEU* 1.3 104.5 - - + +
120I LEU* 1.3 60.7 + - - +
127I PHE* 4.1 5.8 - - + -
128I ILE 5.1 2.9 - - - +
129I ILE* 5.9 0.4 - - + -
382I LEU* 5.8 3.8 - - + -
383I ARG* 6.0 4.0 - - + +
386I PHE* 3.5 41.5 - - + -
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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