Contacts of the strand formed by residues 109 - 118 (chain D) in PDB entry 3CII
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 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D CYS* 4.8 3.8 - - + -
102D GLU 3.7 6.7 - - - -
103D LEU* 3.6 8.2 - - - +
106D ASP* 4.6 5.4 - - - +
108D ARG* 1.3 76.1 - - + +
110D LEU* 1.3 60.7 + - - +
111D ARG* 3.3 27.1 - - - -
112D GLY* 3.3 26.9 - - - -
130D LEU* 4.1 9.2 - - + -
160D LEU* 3.9 14.1 - - + -
161D GLU* 3.9 35.9 - - + +
165D VAL* 3.8 29.6 - - + +
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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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2D SER* 5.6 4.9 - - - +
102D GLU* 2.7 28.5 + - + +
103D LEU 3.5 22.2 - - - +
104D GLY* 3.7 18.2 - - - +
105D PRO* 4.1 11.0 - - + -
106D ASP* 5.2 3.4 - - - +
108D ARG 3.2 1.0 + - - -
109D PHE* 1.3 77.8 - - - +
111D ARG* 1.3 82.3 + - + +
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Residues in contact with ARG 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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102D GLU* 2.9 67.7 + - - +
109D PHE* 3.3 17.8 - - - -
110D LEU* 1.3 95.3 - - + +
112D GLY* 1.3 75.4 + - - +
113D TYR* 3.6 23.6 - - - +
128D GLU* 5.9 6.7 - - - +
58E LYS* 5.6 2.0 - - - +
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Residues in contact with GLY 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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100D GLY 3.6 8.5 - - - -
101D CYS* 4.5 1.3 - - - -
109D PHE* 3.3 18.7 - - - -
111D ARG* 1.3 90.5 + - - +
113D TYR* 1.3 66.0 + - - +
128D GLU* 5.0 6.8 + - - +
130D LEU* 4.2 19.3 - - - +
160D LEU* 4.7 3.8 - - - -
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Residues in contact with TYR 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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6D LYS* 3.4 35.9 - - + +
98D MET* 3.8 33.9 - - + +
99D HIS* 3.5 8.0 - - - -
100D GLY* 3.0 48.6 + - - +
102D GLU* 3.6 19.7 - - + -
111D ARG* 3.6 26.2 - - - +
112D GLY* 1.3 74.5 - - - +
114D GLU* 1.3 72.7 + - - +
115D GLN* 5.6 6.5 - - + +
126D LEU 5.2 3.1 - - - +
130D LEU* 4.6 5.2 - - - -
160D LEU* 3.5 15.5 - - - +
58E LYS* 3.9 15.7 + - - -
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Residues in contact with GLU 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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97D TRP* 3.5 27.2 + - - +
98D MET 3.5 7.0 - - - -
99D HIS* 3.1 24.3 - - + +
113D TYR* 1.3 82.8 - - - +
115D GLN* 1.3 64.3 + - - +
116D PHE* 5.0 0.4 - - + -
125D THR* 3.6 2.1 - - - +
126D LEU* 2.7 51.8 + - + +
133D TRP* 3.1 23.2 - - + -
156D GLN* 2.9 40.3 + - - +
159D TYR* 5.1 0.2 - - - -
160D LEU* 4.4 8.1 - - + +
3F ALA* 5.0 0.5 - - - +
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Residues in contact with GLN 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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97D TRP* 3.6 2.9 - - - -
98D MET* 3.0 46.5 + - - +
113D TYR* 5.6 6.6 - - + +
114D GLU* 1.3 79.0 - - - +
116D PHE* 1.3 64.0 - - - +
122D ASP* 3.8 18.0 + - - +
124D LEU 3.1 16.8 - - - +
125D THR* 3.2 25.3 + - - +
126D LEU 4.6 0.2 - - - +
133D TRP* 5.6 0.4 - - - -
58E LYS 5.8 2.2 + - - -
60E TRP* 3.5 32.3 - - + -
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Residues in contact with PHE 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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74D PHE* 3.8 18.2 - + - -
77D ASN* 5.6 0.2 - - - -
95D LEU* 4.9 5.4 - - + -
96D GLN 3.4 6.5 - - - -
97D TRP* 3.4 47.3 - + + -
114D GLU* 5.4 0.2 - - + -
115D GLN* 1.3 74.5 - - - +
117D ALA* 1.3 63.8 + - - +
122D ASP* 3.8 3.3 - - - +
123D TYR* 2.9 24.5 + - + -
124D LEU* 2.7 39.4 + - + +
133D TRP* 4.2 12.8 - + - -
60E TRP* 3.9 4.1 - - - -
6F THR* 3.7 17.5 - - + -
7F LEU* 3.5 37.0 - - + -
9F LEU* 4.5 16.6 - - + -
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Residues in contact with ALA 117 (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 THR 3.7 0.5 - - - +
95D LEU* 3.3 9.9 - - - +
96D GLN* 3.0 33.7 + - + +
116D PHE* 1.3 79.4 - - - +
118D TYR* 1.3 60.4 + - - +
119D ASP 3.9 0.7 + - - -
120D GLY 5.1 1.1 - - - +
121D LYS 3.5 10.1 - - - +
122D ASP* 3.8 0.7 - - - -
123D TYR* 3.4 8.1 - - - +
60E TRP* 3.2 48.0 - - + +
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Residues in contact with TYR 118 (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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78D LEU* 4.4 18.7 + - + -
81D LEU* 3.4 39.0 - - + -
82D ARG* 4.0 13.9 + - - +
85D TYR* 3.5 31.6 - + - +
87D GLN* 3.2 29.8 + - - -
93D HIS* 3.3 18.2 + - + +
94D THR 3.6 8.1 - - - -
95D LEU* 4.3 3.8 - - + -
117D ALA* 1.3 70.1 - - - +
119D ASP* 1.3 97.4 + - + +
120D GLY 3.4 0.4 - - - -
121D LYS* 2.9 27.5 + - - +
123D TYR* 3.7 21.3 - - + +
0E MET 5.5 0.5 + - - -
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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