Contacts of the strand formed by residues 103 - 112 (chain G) in PDB entry 1U3H
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 ASN 103 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G PRO* 4.4 0.8 - - - +
94G LYS* 3.7 2.9 + - - +
95G SER* 2.9 52.9 + - - -
96G PRO 3.3 14.8 + - - -
97G VAL* 4.1 12.7 - - - +
98G LEU 5.2 0.2 - - - +
101G GLN 4.0 6.2 + - - +
102G PRO* 1.3 75.8 - - - +
104G THR* 1.3 87.1 + - - +
152G THR* 3.4 5.5 - - - -
153G PHE* 2.9 47.3 + - + +
155G PRO* 4.5 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G PRO* 3.5 1.9 - - - +
94G LYS* 2.8 47.6 + - + +
103G ASN* 1.3 88.2 + - - +
105G LEU* 1.3 72.7 + - - +
106G ILE* 4.5 1.8 - - + -
150G TYR* 3.7 32.1 - - + -
151G LEU 3.5 9.9 - - - +
152G THR* 4.3 12.5 - - + +
153G PHE* 3.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G VAL* 3.4 26.7 - - + -
92G PHE 3.6 18.8 - - - +
93G PRO* 3.9 3.8 - - + -
104G THR* 1.3 74.1 - - - +
106G ILE* 1.3 60.1 + - - +
121G TRP* 3.7 21.5 - - + -
150G TYR* 3.3 5.4 - - - -
151G LEU* 2.8 41.7 + - + +
153G PHE* 3.7 16.0 - - + -
161G TYR* 3.5 44.9 - - + -
178G TRP* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G THR 3.7 1.0 - - - +
91G VAL* 3.3 7.1 - - - +
92G PHE* 2.8 78.7 + - + +
94G LYS* 3.9 21.3 - - + -
104G THR* 4.1 7.4 - - + +
105G LEU* 1.3 77.0 - - - +
107G CYS* 1.3 64.5 + - - +
108G PHE 4.0 0.2 - - - -
121G TRP* 3.9 2.5 - - - -
148G LEU* 3.9 21.5 - - + -
149G SER 3.5 4.5 - - - +
150G TYR* 3.6 31.2 - - + -
150H ASN* 3.8 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 107 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G ALA* 4.1 9.2 - - - -
90G THR 3.6 1.8 - - - -
91G VAL* 4.0 6.5 - - - -
106G ILE* 1.3 74.5 - - - +
108G PHE* 1.3 59.7 + - - +
109G VAL* 3.8 19.3 + - - +
119G ILE* 4.5 0.2 - - - -
121G TRP* 3.5 19.2 - - + -
147G LYS 3.8 0.9 - - - +
148G LEU* 3.2 5.0 - - - -
149G SER* 2.8 39.4 + - - +
163G CYS* 2.0 49.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G GLN 3.5 1.2 - - - +
89G ALA* 3.3 2.6 - - - -
90G THR* 2.9 55.0 + - + +
92G PHE* 3.8 20.0 - + + -
106G ILE 4.0 0.8 - - - -
107G CYS* 1.3 72.0 - - - +
109G VAL* 1.3 61.5 + - - +
110G ASP* 3.6 38.6 - - + -
146G HIS* 3.5 31.4 - + + -
147G LYS 3.9 2.2 - - - -
148G LEU* 4.0 24.2 - - + -
149H ARG 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G PRO* 3.6 30.7 - - + -
88G GLN 3.3 8.3 - - - +
89G ALA* 4.3 1.6 - - + -
107G CYS* 4.0 19.7 - - - +
108G PHE* 1.3 77.6 - - - +
110G ASP* 1.3 59.1 + - - +
112G ILE* 3.2 19.1 - - + +
117G ILE* 4.0 7.9 - - + -
119G ILE* 3.7 23.8 - - + -
146G HIS* 2.9 26.1 - - - -
147G LYS 3.0 17.0 + - - +
165G VAL* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G PRO* 3.3 4.2 - - - +
88G GLN* 3.0 35.3 + - + +
108G PHE* 3.6 32.2 - - + -
109G VAL* 1.3 74.7 - - - +
111G ASN* 1.3 84.7 + - + +
112G ILE 3.2 4.1 + - - -
140G ASN* 3.0 24.8 + - - +
146G HIS* 3.6 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G GLU* 3.6 31.3 + - - +
86G ALA 2.9 26.9 + - - +
87G PRO* 3.6 10.9 - - - +
88G GLN* 4.9 4.3 - - + +
110G ASP* 1.3 90.6 + - + +
112G ILE* 1.3 61.7 + - - +
113G PHE 3.6 2.8 + - - -
142G ASP* 4.3 5.7 - - - +
144G SER* 4.0 21.0 + - - -
145G PHE 3.4 2.1 + - - -
34H ARG* 4.2 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G PRO* 4.3 5.2 - - + -
109G VAL* 3.2 46.9 - - + +
110G ASP 3.8 1.8 - - - +
111G ASN* 1.3 71.1 - - - +
113G PHE* 1.3 67.7 + - - +
114G PRO 3.6 14.6 - - - +
115G PRO* 4.5 0.2 - - + -
117G ILE* 4.0 23.3 - - + -
119G ILE* 5.3 0.2 - - + -
137G PHE* 4.0 21.5 - - + -
145G PHE* 2.7 51.3 + - + +
146G HIS* 3.9 1.3 - - - -
147G LYS* 3.7 25.8 - - + +
167G HIS* 4.1 5.6 - - + +
----------------------------------------------------------
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