Contacts of the strand formed by residues 107 - 111 (chain A) in PDB entry 1DS1
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 LEU 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 3.7 30.7 - - - +
106A GLY* 1.3 74.5 - - - -
108A HIS* 1.3 65.5 + - - +
109A THR* 2.9 7.9 + - - +
300A ILE* 3.5 3.7 - - - +
301A ARG* 2.8 42.6 + - + +
308A LEU* 4.0 22.9 - - + -
312A GLU* 3.7 41.1 - - + +
313A ARG* 4.3 3.8 - - - +
314A ALA* 3.9 18.6 - - - +
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Residues in contact with HIS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.7 36.2 - - + +
98A LEU 3.0 30.7 - - - -
99A GLY* 3.7 2.4 + - - -
102A GLY 3.6 1.0 - - - -
103A ARG* 3.6 38.6 + - - +
106A GLY 4.4 0.4 - - - -
107A LEU* 1.3 73.4 - - - +
109A THR* 1.3 60.1 + - - +
119A VAL* 3.8 17.9 - - + -
120A TYR* 4.3 5.4 + - - -
298A VAL* 3.9 19.9 - - + +
299A TYR 3.3 8.3 - - - +
300A ILE* 3.8 18.5 - - + +
301A ARG* 5.6 0.2 + - - -
313A ARG 4.0 1.9 - - - +
314A ALA* 3.6 3.9 - - + +
315A GLY* 2.9 22.8 + - - -
316A ASP* 4.0 2.1 + - - +
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 2.9 15.3 + - - +
108A HIS* 1.3 72.2 + - - +
110A GLY* 1.3 71.7 + - - +
111A TYR* 3.6 35.9 - - + +
119A VAL* 4.5 9.0 - - - +
299A TYR* 2.9 26.0 + - - +
301A ARG* 2.9 47.3 + - - +
316A ASP 3.5 6.1 - - - +
318A VAL* 4.1 6.3 - - + -
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Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 1.3 80.1 - - - +
111A TYR* 1.3 67.0 + - - -
118A THR 3.7 19.5 - - - -
119A VAL* 3.8 12.0 - - - +
121A HIS* 5.6 0.7 - - - -
299A TYR* 5.6 0.7 - - - -
316A ASP 2.9 12.3 + - - -
317A VAL* 3.3 10.7 - - - -
318A VAL* 2.9 21.3 + - - +
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Residues in contact with TYR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 3.6 31.7 - - + +
110A GLY* 1.3 73.4 - - - -
112A ARG* 1.3 66.5 + - - +
113A GLU* 3.2 2.2 - - - -
114A LEU* 2.9 39.4 + - + +
117A GLY* 3.6 2.9 - - - -
118A THR 4.4 2.8 + - - -
121A HIS* 5.8 1.2 + + - -
147A MET* 3.9 13.0 - - + -
150A HIS* 3.5 31.2 - + - -
152A LEU 2.7 30.4 + - - -
154A PRO* 3.3 24.5 - - + +
205A PHE* 4.1 11.4 - - + -
299A TYR* 3.7 31.4 - + + -
301A ARG* 4.2 1.6 - - - +
317A VAL* 4.0 2.0 - - - +
318A VAL* 3.5 19.5 - - + +
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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