Contacts of the strand formed by residues 108 - 113 (chain A) in PDB entry 6D1U
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 TYR 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ILE* 3.6 42.3 - - + +
82A THR 4.5 0.5 + - - -
83A PRO* 4.4 8.1 - - + -
87A PHE* 4.0 12.1 - + - -
96A TRP* 4.2 4.0 - + - -
99A VAL* 4.6 0.2 - - - -
107A ALA* 1.3 72.0 - - - +
109A PRO* 1.3 66.9 - - + +
110A ILE* 3.8 3.8 + - + +
265A SER* 3.2 5.1 - - - -
266A ALA* 2.8 46.3 + - + +
268A ILE* 4.2 8.7 - - + +
279A LYS* 3.6 15.7 - - + +
282A LEU* 3.7 32.1 - - + -
283A GLU* 2.6 44.6 + - + -
287A LEU* 4.0 26.9 - - + -
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Residues in contact with PRO 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.6 18.2 - - + +
95A THR* 3.5 52.7 - - - +
96A TRP* 3.4 26.9 - - + -
99A VAL* 4.1 4.9 - - + -
107A ALA 3.9 3.1 - - - +
108A TYR* 1.3 84.8 - - - +
110A ILE* 1.3 65.6 + - - +
263A VAL* 3.6 10.5 - - + -
264A LEU 3.8 4.3 - - - +
265A SER* 4.1 4.3 - - - +
287A LEU* 3.6 12.8 - - - +
305A ALA* 3.7 2.3 - - + +
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 3.9 19.1 - - + -
108A TYR* 3.9 11.4 - - + +
109A PRO* 1.3 82.3 - - - +
111A ALA* 1.3 61.9 + - + +
264A LEU* 2.7 39.7 + - + +
265A SER* 4.2 1.8 - - - -
266A ALA* 4.3 6.1 - - + +
282A LEU* 5.2 1.1 - - + -
286A LEU* 3.9 24.9 - - + -
287A LEU* 3.8 24.2 - - + +
292A LEU* 4.0 21.9 - - + +
295A VAL* 6.4 0.2 - - + -
301A LEU* 4.4 10.8 - - + -
304A VAL* 3.6 6.2 - - - +
305A ALA* 2.9 22.6 + - - +
306A LEU 4.7 0.5 + - - -
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ILE* 1.3 86.9 - - + +
112A VAL* 1.3 64.5 + - - +
113A GLU* 4.0 0.7 + - - +
263A VAL* 3.3 6.5 - - - +
264A LEU* 2.8 32.5 + - + +
301A LEU* 3.5 41.5 - - + +
303A ALA 3.5 11.2 - - - +
304A VAL* 3.9 4.9 - - + +
305A ALA* 4.0 3.1 - - - +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR* 6.5 0.2 - - + -
94A PHE* 3.7 36.1 - - + -
95A THR* 4.0 14.6 - - + -
111A ALA* 1.3 73.8 - - - +
113A GLU* 1.3 63.3 + - - +
114A ALA 4.4 0.2 + - - -
261A VAL* 3.5 26.7 - - + -
262A GLY 3.6 3.8 - - - +
263A VAL* 4.4 7.2 - - + +
301A LEU 4.5 0.2 - - - -
302A GLY* 3.6 7.1 - - - -
303A ALA* 2.7 43.5 + - + +
304A VAL 5.5 0.7 - - - -
322A THR* 4.5 0.5 - - - +
323A MET* 4.0 24.0 - - + +
326A ALA* 5.0 1.6 - - + -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 3.1 30.0 + - - -
65A ALA* 4.7 12.6 - - - +
111A ALA 4.4 4.7 - - - +
112A VAL* 1.3 78.0 - - - +
114A ALA* 1.3 62.5 + - - +
157A TYR* 4.3 10.8 + - - +
231A PRO* 5.0 4.3 - - + -
232A TRP* 3.6 32.8 - - + -
260A PHE 4.4 0.7 - - - +
261A VAL* 3.5 8.1 - - - +
262A GLY* 2.8 37.5 + - - +
264A LEU* 3.6 23.5 - - + +
301A LEU 4.0 15.4 - - - +
322A THR* 4.9 0.9 - - - -
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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