Contacts of the helix formed by residues 990 - 999 (chain A) in PDB entry 3U44
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 PHE 990 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988A PHE 3.1 0.6 - - - -
989A ALA* 1.3 91.7 - - + +
991A ASP* 1.3 65.1 + - - +
992A GLU 2.8 5.6 + - - -
993A LYS* 3.0 27.7 + - + +
994A ALA* 3.1 11.1 + - - +
709B ASP* 3.5 51.4 - - + -
710B GLU* 5.1 2.7 - - + -
713B LEU* 3.8 35.0 - - + -
741B ASP* 4.5 3.8 - - + -
742B VAL* 4.0 32.3 - - + -
745B SER* 3.3 12.6 + - - +
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Residues in contact with ASP 991 (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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988A PHE* 2.9 38.4 + - - +
989A ALA 3.4 0.2 - - - -
990A PHE* 1.3 76.8 - - - +
992A GLU* 1.3 60.3 + - - +
994A ALA* 4.3 1.7 + - - +
995A ARG* 3.7 18.4 + - - +
745B SER* 3.1 23.4 + - - +
748B ASN* 5.2 8.9 + - - +
749B VAL* 4.7 7.8 - - - +
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Residues in contact with GLU 992 (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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988A PHE 4.8 0.2 + - - -
989A ALA 5.0 1.9 + - - +
990A PHE 2.8 2.2 + - - -
991A ASP* 1.3 79.4 - - - +
993A LYS* 1.3 66.3 + - + +
995A ARG* 3.3 22.5 + - - +
996A GLU* 3.5 19.5 + - - +
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Residues in contact with LYS 993 (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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989A ALA 6.0 0.2 - - - +
990A PHE* 3.0 22.7 + - + +
992A GLU* 1.3 74.5 - - + +
994A ALA* 1.3 67.3 + - - +
995A ARG 3.0 2.8 + - - -
996A GLU* 3.1 30.5 + - + +
997A GLN* 3.1 24.3 + - - +
713B LEU* 3.4 36.3 - - + +
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Residues in contact with ALA 994 (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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990A PHE* 3.1 13.3 + - + +
991A ASP 4.5 0.4 - - - +
993A LYS* 1.3 78.4 - - - +
995A ARG* 1.3 61.6 + - - +
997A GLN* 3.8 4.5 + - - +
998A LEU* 3.4 31.7 + - + +
713B LEU* 4.6 11.9 - - + +
716B VAL* 5.1 5.6 - - + -
742B VAL 4.6 1.6 - - - +
745B SER* 3.8 22.0 - - - -
746B THR* 3.9 23.6 - - - +
749B VAL* 4.2 4.5 - - + -
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Residues in contact with ARG 995 (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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991A ASP* 3.7 13.9 + - - +
992A GLU* 3.3 20.8 + - - +
993A LYS 3.0 0.6 - - - -
994A ALA* 1.3 80.4 - - - +
996A GLU* 1.3 58.9 + - - +
998A LEU* 3.8 2.5 + - - +
999A SER* 3.0 32.0 + - - +
749B VAL* 4.1 31.1 - - + +
752B SER* 5.5 5.5 + - - -
753B GLU* 5.8 5.8 + - - +
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Residues in contact with GLU 996 (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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992A GLU* 3.5 17.9 + - - +
993A LYS* 3.1 31.5 + - - +
995A ARG* 1.3 78.4 - - + +
997A GLN* 1.3 66.7 + - + +
998A LEU 3.2 0.4 - - - -
999A SER* 2.9 11.5 + - - +
1000A TRP* 2.8 29.2 + - - +
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Residues in contact with GLN 997 (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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993A LYS* 3.1 20.1 + - - +
994A ALA 4.4 1.1 - - - +
996A GLU* 1.3 82.6 - - + +
998A LEU* 1.3 61.5 + - - +
1000A TRP* 3.4 20.6 + - - +
336B ARG* 4.2 26.5 + - - +
713B LEU* 3.5 40.1 + - - +
714B MET* 5.3 1.2 - - - -
716B VAL* 3.3 32.5 - - + +
717B VAL* 4.1 14.2 + - - +
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Residues in contact with LEU 998 (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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994A ALA* 3.4 15.7 + - + +
995A ARG* 4.2 4.9 - - - +
996A GLU 3.2 0.4 - - - -
997A GLN* 1.3 77.5 - - - +
999A SER* 1.3 56.4 + - - +
1000A TRP 3.3 3.1 + - - +
716B VAL* 3.7 23.1 - - + +
717B VAL 5.5 0.4 - - - -
718B ASN* 3.8 26.0 - - - +
719B LYS* 3.8 12.4 + - + +
722B ALA* 3.9 9.9 - - + -
746B THR* 4.4 15.0 - - + -
749B VAL* 3.6 34.3 - - + -
750B LEU* 4.1 18.4 - - + -
753B GLU* 5.5 4.0 - - - +
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Residues in contact with SER 999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995A ARG* 3.0 35.6 + - - +
996A GLU* 2.9 19.1 + - - +
998A LEU* 1.3 76.8 - - - +
1000A TRP* 1.3 65.8 + - - +
1001A THR* 4.2 6.6 + - - +
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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