Contacts of the strand formed by residues 385 - 390 (chain B) in PDB entry 1TTT
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 385 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ARG* 2.7 72.3 + - - +
125B GLN* 3.4 21.3 - - - +
127B GLY* 5.0 9.2 - - - +
128B VAL 5.8 1.2 + - - -
343B TYR 4.3 1.9 - - - +
344B PHE* 4.4 4.5 - - - -
345B ARG 5.0 1.2 + - - -
383B GLY 3.4 8.5 + - - +
384B LEU* 1.3 92.1 - - - +
386B PHE* 1.3 64.6 + - - +
398B GLY 3.3 13.0 - - - +
399B VAL* 3.7 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLN* 2.8 28.3 + - - -
316B PHE* 4.0 11.0 - + - -
318B ALA* 3.6 23.8 - - + -
320B VAL* 4.2 4.9 - - + -
342B PHE* 3.8 25.8 - + - -
343B TYR 3.1 19.3 - - - +
344B PHE* 3.7 25.6 - + + -
372B VAL* 5.7 0.2 - - + -
384B LEU 4.0 1.1 - - - -
385B ARG* 1.3 77.9 - - - +
387B ALA* 1.3 72.9 + - - +
388B ILE* 4.1 15.3 - - + -
398B GLY* 2.9 23.8 + - - -
399B VAL* 3.2 35.7 - - - -
400B VAL 3.5 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 4.0 23.1 - - + -
125B GLN* 3.9 17.5 - - + +
341B GLN 3.7 0.3 - - - +
342B PHE* 3.5 5.9 - - - -
343B TYR* 3.1 41.0 + - + +
386B PHE* 1.3 77.8 - - - +
388B ILE* 1.3 70.2 + - - +
389B ARG* 5.4 1.6 - - + -
394B THR* 4.9 1.1 - - + -
396B GLY 3.6 8.5 - - - +
397B ALA* 4.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B VAL* 4.1 20.6 - - + -
322B ILE* 4.9 4.0 - - + -
334B PHE* 6.5 0.2 - - + -
338B TYR* 5.5 0.4 - - + -
340B PRO* 3.8 24.0 - - + -
341B GLN 3.5 9.6 - - - +
342B PHE* 3.7 23.6 - - + -
353B VAL* 6.4 0.4 - - + -
370B PHE* 4.7 10.5 - - + -
386B PHE* 4.1 12.8 - - + -
387B ALA* 1.3 80.3 - - - +
389B ARG* 1.3 60.2 + - - +
394B THR* 3.4 5.4 - - - +
395B VAL* 2.5 43.7 + - + -
396B GLY* 2.8 30.6 + - - +
397B ALA 4.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA 4.4 4.4 + - - -
87B ASP* 6.1 0.6 - - - +
89B ILE* 3.6 37.1 - - - +
90B LYS 5.4 1.0 - - - +
93B ILE* 4.4 5.4 - - - +
118B GLU* 2.5 32.9 + - - -
122B LEU* 4.7 6.1 - - + -
340B PRO* 3.8 0.3 - - - +
341B GLN* 3.0 31.7 + - - +
343B TYR* 3.8 32.6 + - + +
387B ALA* 4.1 1.3 - - + -
388B ILE* 1.3 74.2 - - - +
390B GLU* 1.3 68.1 + - - +
392B GLY* 3.5 24.5 + - - +
393B ARG* 2.9 14.5 - - - +
394B THR* 3.0 45.4 + - + +
395B VAL* 3.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ARG* 3.6 11.6 + - - +
338B TYR* 2.7 35.4 + - + +
339B ARG 4.9 2.2 - - - +
340B PRO* 3.6 26.2 - - + -
341B GLN* 3.7 8.3 - - - +
389B ARG* 1.3 79.9 - - - +
391B GLY* 1.3 81.1 + - - +
392B GLY 3.3 2.5 - - - -
393B ARG* 2.6 26.4 + - - +
395B VAL* 4.2 7.2 - - + +
51E G 3.2 29.3 + - - +
52E U 4.0 10.4 + - - +
63E C 4.3 0.2 - - - +
64E A 3.9 6.7 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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