Contacts of the helix formed by residues 113 - 127 (chain L) in PDB entry 5NSS
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 PRO 113 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70L GLU* 5.5 13.2 - - + -
74L ASP* 6.6 0.2 - - + -
111L THR 4.0 0.4 - - - -
112L ALA* 1.3 79.2 - - - +
114L MET* 1.3 65.0 + - - +
115L MET* 3.1 13.2 + - + +
116L VAL* 3.4 14.5 + - + +
117L GLN* 3.7 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L ALA 3.9 0.2 + - - -
113L PRO* 1.3 71.6 - - - +
115L MET* 1.3 58.6 + - - +
116L VAL 3.3 0.2 - - - -
117L GLN* 3.6 9.0 - - - +
118L GLU* 2.9 31.0 + - - +
160L THR 5.2 7.0 - - - +
161L PHE* 6.1 0.2 - - - -
162L ARG* 4.5 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 115 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66K ALA* 4.0 20.2 - - - +
67K ALA 6.0 0.2 - - - +
74L ASP* 5.0 13.2 - - + -
113L PRO* 3.1 9.4 - - + +
114L MET* 1.3 79.4 - - - +
116L VAL* 1.3 57.7 + - - +
118L GLU* 4.0 2.8 - - - -
119L LYS* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65L CYS* 6.5 0.2 - - + -
73L LEU* 4.5 22.9 - - + +
74L ASP* 4.5 13.8 - - + +
77L LEU* 4.9 9.2 - - + +
112L ALA* 5.1 10.8 - - + -
113L PRO* 3.4 11.9 + - + +
114L MET 3.3 0.2 - - - -
115L MET* 1.3 77.9 - - - +
117L GLN* 1.3 59.1 + - - +
119L LYS* 4.4 5.2 - - - -
120L LEU* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L PRO 3.7 4.1 + - - +
114L MET* 3.3 17.3 + - - +
115L MET 3.2 0.6 - - - -
116L VAL* 1.3 79.7 - - - +
118L GLU* 1.3 58.2 + - - +
120L LEU* 3.9 3.5 - - - +
121L LEU* 2.9 30.9 + - - +
162L ARG* 4.8 14.1 - - + +
164L ASP* 5.0 3.1 - - + +
165L LEU* 5.0 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66K ALA* 3.7 27.1 - - + -
108K GLU* 5.3 7.6 - - + -
111K THR* 6.0 0.9 - - - -
114L MET 2.9 16.7 + - - +
115L MET 4.1 0.4 - - - +
117L GLN* 1.3 74.3 - - - +
119L LYS* 1.3 61.3 + - - +
121L LEU* 3.8 5.2 - - - +
122L ARG* 2.9 32.1 + - - +
164L ASP* 5.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K ASN* 5.7 0.2 - - - -
67K ALA* 3.7 35.5 - - + +
77L LEU* 5.7 1.1 - - + -
78L PHE* 3.8 25.1 - - + +
115L MET 2.9 19.7 + - - +
116L VAL* 4.1 4.3 - - - +
118L GLU* 1.3 77.2 - - - +
120L LEU* 1.3 56.6 + - - +
122L ARG* 4.3 2.1 - - - +
123L VAL* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77L LEU* 5.3 14.1 + - + +
116L VAL 2.9 21.0 + - - +
117L GLN* 4.2 3.1 - - - +
119L LYS* 1.3 77.3 - - - +
121L LEU* 1.3 52.4 + - - +
123L VAL* 4.7 2.5 - - - -
124L ILE* 2.6 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117L GLN 2.9 21.7 + - - +
118L GLU* 3.8 5.2 - - - +
119L LYS 3.3 0.2 - - - -
120L LEU* 1.3 75.5 - - - +
122L ARG* 1.3 59.1 + - - +
124L ILE* 4.2 1.9 - - - +
125L GLU* 2.9 31.0 + - - +
164L ASP* 4.0 24.0 - - + -
168L ARG* 6.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K ASN* 4.3 23.6 - - + -
107K ASP* 5.1 11.4 - - + -
118L GLU 2.9 17.2 + - - +
119L LYS 4.3 1.3 - - - +
121L LEU* 1.3 76.0 - - - +
123L VAL* 1.3 59.7 + - - +
125L GLU* 3.4 4.2 + - - +
126L TYR* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77L LEU 5.6 5.8 - - - +
78L PHE* 6.2 1.8 - - - +
119L LYS 2.9 20.2 + - - +
120L LEU* 4.6 2.5 - - - +
122L ARG* 1.3 77.1 - - - +
124L ILE* 1.3 56.9 + - - +
126L TYR* 4.6 2.2 - - - +
127L GLY* 2.8 24.1 + - - -
128L GLU 3.2 30.0 + - - +
129L LEU* 4.6 6.7 - - - -
130L GLU* 4.8 7.6 - - + +
140L VAL 4.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120L LEU* 2.6 24.9 + - + +
121L LEU* 4.2 2.7 - - - +
123L VAL* 1.3 74.7 - - - +
125L GLU* 1.3 65.5 + - - +
127L GLY* 3.5 9.7 + - - +
140L VAL 5.4 2.9 - - - -
141L ASN* 6.1 0.3 - - - -
142L VAL 5.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121L LEU 2.9 21.9 + - - +
122L ARG* 3.9 5.4 - - - +
124L ILE* 1.3 78.7 - - - +
126L TYR* 1.3 59.5 + - - +
127L GLY* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122L ARG 2.9 17.9 + - - +
123L VAL* 4.2 3.6 - - - +
125L GLU* 1.3 77.4 - - - +
127L GLY* 1.3 61.0 + - - +
128L GLU* 3.5 10.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L VAL 2.8 9.5 + - - -
124L ILE 3.5 7.6 + - - -
125L GLU 3.4 3.0 - - - -
126L TYR* 1.3 77.7 - - - +
128L GLU* 1.3 53.0 + - - +
139L GLN* 3.4 9.7 - - - +
140L VAL 2.8 40.7 + - - +
141L ASN* 4.7 9.4 - - - +
----------------------------------------------------------
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