Contacts of the strand formed by residues 142 - 150 (chain B) in PDB entry 3NCF
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 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B PRO* 4.0 13.7 - - + -
129B PRO* 4.1 4.7 - - + -
130B PRO* 3.8 25.4 - - + -
133B ILE* 4.1 21.1 - - + -
135B LEU* 3.7 14.3 - - + +
140B PHE* 3.4 22.7 - - + -
141B THR* 1.3 73.8 - - - +
143B LEU* 1.3 62.6 + - - +
144B TYR* 3.7 26.2 - - + +
163B GLN* 3.4 28.5 + - - +
184B CYS* 4.0 15.0 - - + -
185B LYS 3.4 20.2 - - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A HIS* 5.1 12.6 - - + +
141B THR* 5.2 4.9 - - + -
142B LEU* 1.3 74.8 - - - +
144B TYR* 1.3 62.4 + - - +
160B PHE* 4.1 27.6 - - + -
162B GLY* 3.2 12.3 - - - +
163B GLN* 3.5 33.0 - - + +
184B CYS* 3.0 6.1 - - - +
185B LYS* 2.8 59.9 + - + +
186B PRO 4.6 7.6 - - - +
187B ASP* 4.9 8.5 - - - +
191B TRP* 3.7 1.9 - - - -
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PRO* 4.1 11.9 - - + -
127B TRP* 3.2 44.9 - + + -
129B PRO* 3.5 30.4 - - + +
135B LEU* 4.7 3.6 - - - +
142B LEU* 3.7 25.6 - - + +
143B LEU* 1.3 74.9 - - - +
145B GLU* 1.3 61.0 + - - +
160B PHE* 3.8 8.7 - - - -
161B ALA* 3.0 24.8 + - + -
162B GLY 2.8 22.1 + - - +
163B GLN 4.2 8.7 - - - -
164B GLN 3.2 23.1 - - - -
165B THR* 4.0 11.2 - - + +
182B VAL* 4.5 2.5 - - + -
183B ARG 3.4 6.3 - - - +
184B CYS* 3.6 24.5 - - + -
191B TRP* 4.3 2.9 - - - -
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B TYR* 1.3 72.8 - - - +
146B ILE* 1.3 63.4 - - - +
158B ILE* 3.6 26.1 - - + +
159B HIS 3.8 6.7 - - - +
160B PHE* 4.3 14.6 - - + +
161B ALA 5.4 0.2 - - - -
182B VAL* 3.2 7.8 - - - +
183B ARG* 2.7 74.1 + - + -
191B TRP* 3.7 26.3 - - + -
194B TRP* 3.7 8.5 - - + -
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Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ILE* 4.0 17.9 - - + -
127B TRP* 3.5 39.7 - - + -
145B GLU* 1.3 75.8 - - - +
147B ARG* 1.3 73.3 + - - +
148B LEU* 4.4 12.6 - - + -
157B GLU 3.8 0.2 - - - +
158B ILE* 3.6 5.4 - - - +
159B HIS* 3.1 36.3 + - + +
161B ALA* 4.5 4.9 - - + -
167B PHE* 3.6 26.2 - - + -
169B ILE* 4.6 2.9 - - + -
180B VAL* 4.1 12.8 - - + -
181B GLN 3.4 8.7 - - - +
182B VAL* 4.3 7.0 - - + -
194B TRP* 4.0 2.2 - - - -
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ILE* 1.3 77.9 - - - +
148B LEU* 1.3 65.6 + - - +
156B TRP* 3.6 51.4 - - + +
157B GLU 3.3 9.4 - - - +
158B ILE* 3.9 11.2 - - + -
179B LEU 3.8 0.2 - - - +
180B VAL* 3.3 1.9 - - - +
181B GLN* 2.7 71.0 + - + +
194B TRP* 3.4 59.4 - - + +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 4.4 9.4 - - + -
125B ILE* 5.6 0.2 - - + -
146B ILE* 4.4 3.6 - - + -
147B ARG* 1.3 80.4 - - - +
149B LYS* 1.3 61.8 + - - +
156B TRP* 3.5 3.1 - - - -
157B GLU* 2.9 58.3 + - + +
159B HIS* 4.1 7.2 - - + +
169B ILE* 3.5 30.5 - - + -
172B LEU* 4.2 15.9 - - + -
178B TYR* 3.8 25.9 - - + -
179B LEU 3.0 13.7 - - - +
180B VAL* 3.9 20.9 - - + -
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LEU* 1.3 74.9 - - - +
150B PRO* 1.3 86.5 + - + +
151B GLU* 4.1 2.3 + - - +
152B LYS 3.8 7.1 - - - +
153B ALA* 2.8 34.0 + - + +
154B ALA 4.6 2.0 - - - -
155B GLU 3.3 36.3 - - - +
156B TRP* 3.4 45.1 - - + +
178B TYR* 3.7 5.9 - - - -
179B LEU* 2.7 33.9 + - + +
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Residues in contact with PRO 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LYS* 1.3 99.7 + - + +
151B GLU* 1.3 70.1 + - - +
152B LYS 3.2 0.2 + - - -
153B ALA* 3.1 29.7 + - + +
173B HIS* 5.4 4.5 - - + +
176B GLN* 3.4 36.8 - - + +
177B LYS 3.3 20.6 - - - +
178B TYR* 3.7 18.4 - - + +
179B LEU* 5.2 0.4 - - - -
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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