Contacts of the strand formed by residues 109 - 116 (chain D) in PDB entry 3Q2S
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 ILE 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D LEU* 5.7 1.3 - - + -
98D THR* 4.0 33.0 - - + +
101D VAL* 4.4 24.2 - - + -
106D VAL* 5.4 2.3 - - + +
107D ASN* 4.2 15.4 - - - +
108D ASP* 1.3 78.1 - - - +
110D LEU* 1.3 62.7 + - - +
112D ILE* 4.1 16.2 - - + -
129D VAL* 3.6 30.5 - - + -
130D GLY 3.5 4.0 - - - +
131D VAL* 4.2 7.9 - - + +
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ASP 2.9 24.1 + - - +
109D ILE* 1.3 76.1 - - - +
111D GLU* 1.3 66.8 + - + +
130D GLY* 2.5 18.6 + - - +
131D VAL 4.4 2.7 - - - +
132D GLY* 3.6 25.4 - - - +
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ARG* 3.6 27.9 + - - -
153A PHE* 4.9 4.5 - - - -
110D LEU* 1.3 81.9 - - + +
112D ILE* 1.3 82.9 + - - +
113D LYS* 4.4 9.6 + - - +
128D LEU 5.2 0.2 - - - -
130D GLY* 2.6 41.6 + - - +
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ASP* 4.7 15.1 - - + +
97D LEU* 4.5 19.3 - - + -
98D THR* 4.0 20.4 - - - +
109D ILE* 4.1 21.5 - - + -
111D GLU* 1.3 94.8 + - - +
113D LYS* 1.3 66.7 + - - +
114D PHE* 3.9 30.2 + - + -
127D ALA* 4.5 7.2 - - + -
128D LEU 4.0 3.8 - - - -
129D VAL* 3.6 17.3 - - + -
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ARG* 4.6 14.1 - - - +
152A ASN* 4.1 23.5 - - - +
153A PHE* 5.2 2.2 - - - +
154A GLU* 3.1 34.8 + - - +
111D GLU* 4.4 8.9 + - - +
112D ILE* 1.3 74.8 + - - +
114D PHE* 1.3 84.8 + - - +
115D PHE* 5.3 9.9 - - + -
116D GLU* 6.3 0.2 - - + -
127D ALA* 3.0 14.8 - - - +
128D LEU* 2.9 31.3 + - + +
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Residues in contact with PHE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASN* 5.5 1.3 + - - +
164A HIS* 4.1 32.8 - + + -
165A ILE* 6.0 2.7 - - + -
88D LEU* 4.8 16.2 - - + -
89D THR 6.1 0.2 - - - -
92D THR* 3.6 24.2 - - + -
93D THR 3.9 7.0 - - - -
94D ASP* 3.8 28.5 - - + -
97D LEU* 4.2 16.4 - - + -
112D ILE* 3.9 15.0 + - + -
113D LYS* 1.3 101.0 - - - +
115D PHE* 1.3 65.6 + - - +
116D GLU* 4.0 9.6 + - - +
123D SER* 3.8 20.0 - - - +
126D PHE 4.2 5.2 - - - -
127D ALA* 3.6 17.5 - - + -
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TYR* 3.5 23.8 - + - -
113D LYS* 4.8 5.6 - - + -
114D PHE* 1.3 76.4 - - - +
116D GLU* 1.3 56.0 + - - +
123D SER* 3.7 7.1 + - - -
124D LYS* 2.7 37.0 + - + +
126D PHE* 3.1 62.6 + + + +
128D LEU* 3.1 38.8 - - + -
164D LEU* 4.4 12.8 - - + -
168D GLU* 4.7 8.1 - - - -
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PRO* 4.1 10.8 - - - +
152A ASN* 3.0 37.4 + - - +
154A GLU* 5.4 1.1 - - - +
156A PRO* 4.5 5.4 - - - +
158A TYR* 3.6 18.5 + - - -
164A HIS* 3.7 22.4 + - + +
114D PHE 4.5 8.5 - - - +
115D PHE* 1.3 75.2 - - - +
117D ASN* 1.3 68.4 + - - +
118D ARG* 3.5 7.5 + - + +
121D GLY* 3.8 13.9 - - - +
122D GLN 3.0 15.9 - - - +
124D LYS* 3.2 17.6 + - - +
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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