Contacts of the strand formed by residues 292 - 298 (chain A) in PDB entry 3DRB
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 ARG 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ARG* 3.0 32.5 - - - +
131A VAL* 3.5 1.7 - - - -
132A ARG* 2.9 54.7 + - + +
290A GLY 4.0 1.7 + - - +
291A LEU* 1.3 75.8 - - - +
293A ALA* 1.3 59.4 + - - +
294A GLY* 4.1 3.1 + - - -
318A GLN* 6.1 0.4 - - - +
320A ARG* 3.1 35.6 - - - +
335A ASP* 2.6 40.3 + - - -
337A SER* 3.5 27.2 + - - +
338A ASN* 3.6 2.2 - - - -
341A ARG* 3.7 23.5 - - - +
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Residues in contact with ALA 293 (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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130A ARG 3.3 6.1 - - - -
131A VAL* 4.1 17.5 - - + +
246A MET* 4.7 6.1 - - + -
291A LEU* 3.4 14.5 - - + +
292A ARG* 1.3 73.6 - - - +
294A GLY* 1.3 57.3 + - - +
337A SER* 2.9 21.5 - - - -
338A ASN* 2.6 19.7 + - - +
350A VAL* 4.1 14.6 - - + -
353A VAL* 3.3 16.9 - - + +
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Residues in contact with GLY 294 (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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129A SER* 3.5 2.4 - - - -
130A ARG* 2.9 40.6 + - - +
246A MET* 3.7 4.3 - - - +
292A ARG* 4.1 5.5 + - - +
293A ALA* 1.3 75.1 - - - +
295A VAL* 1.3 65.7 + - - +
335A ASP* 4.7 5.4 - - - -
336A VAL 3.0 13.2 - - - -
337A SER* 3.7 5.6 - - - -
353A VAL* 4.5 3.4 - - - -
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Residues in contact with VAL 295 (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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121A LEU* 4.1 13.5 - - + -
126A VAL* 3.8 22.9 - - + -
128A SER 3.2 7.9 - - - +
129A SER* 3.9 10.8 - - - +
130A ARG* 6.1 1.6 - - - -
246A MET* 3.9 12.1 - - + -
294A GLY* 1.3 79.5 - - - +
296A HIS* 1.3 57.9 + - - +
297A ILE* 3.9 23.8 - - + -
334A PHE 3.2 4.0 - - - +
335A ASP* 3.4 6.2 + - - +
336A VAL* 2.9 37.7 + - + +
353A VAL* 4.7 0.4 - - + -
357A VAL* 3.8 27.8 - - + -
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Residues in contact with HIS 296 (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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126A VAL* 3.6 1.6 - - - -
127A LEU* 2.7 40.6 + - - +
128A SER* 2.9 31.7 + - - +
130A ARG* 5.8 7.4 - - - +
295A VAL* 1.3 68.4 - - - +
297A ILE* 1.3 59.2 + - - +
322A THR* 3.5 32.2 - - + +
326A ASP* 3.0 33.9 + - + -
333A VAL* 3.4 21.1 - - + +
334A PHE 3.5 3.6 - - - -
335A ASP* 4.8 5.8 - - + +
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Residues in contact with ILE 297 (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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125A TYR* 3.3 15.3 - - + +
126A VAL* 4.2 5.6 - - + +
295A VAL* 3.9 19.5 - - + -
296A HIS* 1.3 74.8 - - - +
298A LYS* 1.3 73.2 + - - +
299A LEU* 3.5 35.7 + - + -
333A VAL* 3.3 5.4 - - - +
334A PHE* 2.8 49.7 + - - +
336A VAL* 4.0 11.7 - - + -
357A VAL* 4.1 20.0 - - + +
360A LEU* 4.9 3.6 - - + -
361A ILE* 4.0 22.0 - - + -
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Residues in contact with LYS 298 (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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123A PRO 5.6 0.2 + - - -
124A ASN* 3.0 30.9 + - - +
125A TYR* 2.8 34.9 + - + +
127A LEU* 3.8 36.7 - - + +
297A ILE* 1.3 71.1 - - - +
299A LEU* 1.3 70.2 + - - +
300A PRO* 3.5 6.2 - - + +
330A VAL* 3.4 35.4 - - + +
332A GLY 3.7 5.6 - - - -
333A VAL* 3.9 9.0 - - + -
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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