Contacts of the strand formed by residues 107 - 112 (chain A) in PDB entry 3Q29
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ILE* 3.6 38.6 - - + +
81A THR 4.5 0.3 + - - -
82A PRO* 4.2 10.4 - - + +
86A PHE* 3.7 22.2 - + - -
95A TRP* 4.0 8.1 - + - -
106A ALA* 1.3 71.2 - - - +
108A PRO* 1.3 67.8 - - + +
109A ILE* 3.7 4.6 + - + +
264A SER* 3.2 3.1 - - - -
265A ALA* 2.8 46.1 + - + +
267A ILE* 4.3 7.1 - - + +
278A LYS* 3.5 16.5 - - + +
281A LEU* 3.6 32.3 - - + -
282A GLU* 2.6 43.7 + - + -
286A LEU* 4.1 17.0 - - + -
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Residues in contact with PRO 108 (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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90A LEU* 3.6 25.3 - - + +
94A THR* 3.4 52.0 - - - +
95A TRP* 3.4 29.8 - - + -
98A VAL* 3.7 5.6 - - + -
106A ALA 3.5 4.3 - - - +
107A TYR* 1.3 85.2 - - + +
109A ILE* 1.3 65.4 + - - +
262A VAL* 3.8 7.2 - - + -
263A LEU 3.9 4.7 - - - +
264A SER* 4.1 5.6 - - - +
286A LEU* 3.9 4.7 - - - +
304A ALA* 3.7 3.7 - - + +
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Residues in contact with ILE 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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62A PHE* 3.9 21.3 - - + -
107A TYR* 3.7 13.0 - - + +
108A PRO* 1.3 82.4 - - - +
110A ALA* 1.3 61.6 + - - +
263A LEU* 2.7 29.4 + - + +
264A SER* 4.2 1.3 - - - -
265A ALA* 4.4 4.5 - - + -
281A LEU* 5.4 0.7 - - + -
285A LEU* 3.8 25.8 - - + -
286A LEU* 4.1 17.4 - - + +
291A LEU* 4.1 22.1 - - + +
300A LEU* 4.1 24.2 - - + -
303A VAL* 3.4 6.6 - - - +
304A ALA* 2.8 24.2 + - - +
305A LEU 4.7 0.3 + - - -
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Residues in contact with ALA 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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109A ILE* 1.3 83.2 - - + +
111A VAL* 1.3 65.1 + - - +
112A GLU* 4.5 0.6 - - - +
262A VAL* 3.2 7.6 - - - +
263A LEU* 2.8 32.2 + - + +
300A LEU* 3.4 46.2 - - + +
302A ALA 3.5 6.5 - - - +
303A VAL* 3.9 9.0 - - - +
304A ALA* 4.1 2.8 - - - +
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Residues in contact with VAL 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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93A PHE* 4.1 9.6 - - + -
94A THR* 4.0 16.6 - - + -
110A ALA* 1.3 74.1 - - - +
112A GLU* 1.3 64.7 + - - +
113A ALA 4.4 0.2 + - - -
260A VAL* 3.7 25.8 - - + -
261A GLY 3.4 3.4 - - - +
262A VAL* 4.4 4.5 - - + -
301A GLY* 3.8 6.6 - - - -
302A ALA* 2.8 38.5 + - - +
321A THR* 4.5 5.3 - - + +
322A MET* 3.9 23.1 - - + -
325A ALA* 4.7 2.7 - - + -
376C MET* 3.9 24.7 - - - -
379C LEU* 4.1 7.4 - - + -
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Residues in contact with GLU 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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16A LYS* 2.9 23.6 + - - +
64A ALA* 4.7 4.3 - - - +
110A ALA 4.5 4.5 - - - +
111A VAL* 1.3 78.2 - - - +
113A ALA* 1.3 65.2 + - - +
156A TYR* 4.5 7.0 + - - +
230A PRO* 5.1 3.8 - - + -
231A TRP* 3.9 17.3 - - + -
259A PHE 4.0 0.2 - - - +
260A VAL* 3.5 7.6 - - - +
261A GLY* 2.7 38.4 + - - +
263A LEU* 3.7 28.5 - - + +
300A LEU 4.0 16.2 - - - +
321A THR* 4.7 1.6 - - - -
1B GLC 2.6 32.6 + - - -
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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