Contacts of the strand formed by residues 98 - 103 (chain C) in PDB entry 3U1K
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 98 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C MET* 3.3 16.8 + - + -
97C PRO* 1.3 76.0 - - - +
99C VAL* 1.3 76.6 + - - +
100C VAL* 4.8 0.9 - - + -
135C ASP* 4.0 9.1 - - - +
138C ILE* 4.3 18.6 - - + -
139C ARG* 3.1 59.4 + - + +
142C PHE* 3.9 27.4 - - + -
150C THR* 3.3 28.9 - - + +
152C VAL* 4.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ILE* 5.4 3.8 - - + -
439B LYS* 4.8 12.8 - - - +
97C PRO 6.0 0.2 - - - -
98C LEU* 1.3 78.5 - - - +
100C VAL* 1.3 69.9 + - - +
101C ASP* 3.7 19.3 - - - +
135C ASP* 5.0 1.6 - - - -
149C ASP* 5.7 3.4 - - - +
150C THR 3.0 16.2 + - - +
151C GLN* 3.3 24.9 - - + +
152C VAL 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 4.8 2.9 - - + -
99C VAL* 1.3 81.3 - - - +
101C ASP* 1.3 70.9 + - - +
102C TYR 4.4 2.7 - - - +
131C SER* 3.4 37.3 + - - +
134C ILE* 3.6 29.2 - - + -
135C ASP* 3.7 35.8 + - + +
138C ILE* 3.9 19.7 - - + -
152C VAL* 3.3 16.6 - - + +
154C CYS* 4.7 1.3 - - - -
445C ARG* 5.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B LYS* 5.3 1.9 + - - -
440B VAL* 3.9 16.7 - - + +
99C VAL* 3.7 17.8 - - - +
100C VAL* 1.3 79.0 - - - +
102C TYR* 1.3 61.8 + - - +
103C ARG* 3.8 7.7 + - + +
131C SER* 3.9 1.7 + - - -
151C GLN* 3.1 26.3 + - - +
152C VAL 2.8 10.4 + - - -
153C LEU* 3.6 21.9 - - + +
154C CYS* 3.0 23.7 + - - +
445C ARG* 4.8 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C VAL* 4.0 0.8 - - - +
101C ASP* 1.3 72.7 - - - +
103C ARG* 1.3 73.7 + - - +
104C GLN* 4.7 10.5 + - - -
123C THR* 5.1 0.7 - - - +
126C LYS* 4.6 8.0 - - + -
127C GLU* 3.4 33.3 - - + +
130C THR* 3.5 36.6 - - + -
131C SER* 3.0 26.2 + - - +
134C ILE* 4.0 4.7 - - + -
154C CYS* 3.9 17.7 - - + -
156C LEU* 3.7 23.8 - - + +
165C PRO* 3.4 29.0 - - - +
166C ASP* 3.8 8.8 + - + +
169C ALA* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B GLU* 2.5 41.4 + - - -
430B PRO* 5.4 7.1 - - - +
432B TYR* 6.1 0.6 - - - -
440B VAL* 3.8 49.7 + - - +
101C ASP* 4.5 9.6 - - + +
102C TYR* 1.3 85.7 - - - +
104C GLN* 1.3 63.5 + - - +
105C LYS* 5.6 0.9 - - - +
123C THR* 4.6 13.0 - - + +
127C GLU* 3.3 10.8 - - - +
153C LEU* 4.1 14.1 - - - +
154C CYS 3.7 20.3 + - - +
155C ASN* 4.8 0.2 - - - -
156C LEU* 3.7 22.7 + - - +
----------------------------------------------------------
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