Contacts of the strand formed by residues 162 - 175 (chain A) in PDB entry 4N41
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 ALA 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ALA* 6.0 2.5 - - + -
16A LEU 3.8 12.1 - - - +
18A PRO* 3.7 22.9 - - + -
19A LEU* 3.9 5.8 - - - -
157A VAL* 3.4 1.7 - - - -
158A SER* 2.8 36.5 + - - +
160A SER* 4.4 6.5 - - - +
161A GLY* 1.3 79.4 - - - +
163A PHE* 1.3 68.1 + - - +
164A LEU* 6.2 0.2 - - + -
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Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 3.8 1.9 - - - -
16A LEU* 3.0 39.9 + - + +
17A ARG* 3.2 27.7 + - + +
19A LEU* 3.9 19.0 - - + +
23A GLU* 4.0 19.5 - - - -
67A TRP* 4.0 26.5 - + - -
113A ALA* 3.7 21.3 - - + -
116A LEU* 5.6 3.6 - - + -
155A LEU* 3.5 29.4 - - + -
156A TRP 3.4 9.0 - - - -
157A VAL* 4.5 0.4 - - + -
162A ALA* 1.3 77.7 - - - +
164A LEU* 1.3 63.8 + - - +
303A LEU* 3.6 38.1 - - + -
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 4.5 14.1 - - + +
14A PHE 3.5 21.3 - - - +
15A ALA* 4.1 6.5 - - + -
154A ASP 3.8 0.3 - - - +
155A LEU* 3.2 9.0 - - - +
156A TRP* 2.9 76.8 + - + +
158A SER* 3.9 25.8 - - - -
162A ALA* 3.7 0.4 + - + -
163A PHE* 1.3 78.6 - - - +
165A LEU* 1.3 60.1 + - - +
309A VAL* 4.0 18.4 - - + -
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.0 7.7 - - - +
14A PHE* 2.8 42.1 + - + +
16A LEU* 4.1 20.8 - - + +
117A LEU* 5.4 2.0 - - + -
153A LEU* 4.5 7.4 - - + -
154A ASP 3.5 10.8 - - - +
155A LEU* 4.0 7.0 - - + -
156A TRP* 4.7 0.9 - - - -
164A LEU* 1.3 72.7 - - - +
166A GLU* 1.3 83.5 + - - +
167A VAL* 3.6 17.5 - - + -
294A ALA* 4.0 16.4 - - + +
297A ILE* 3.5 31.4 - - + -
298A GLY 5.0 0.7 - - - +
301A LEU* 4.7 6.3 - - + -
306A PRO* 4.5 11.9 - - + -
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Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASN* 3.7 23.0 + - - +
13A ARG* 4.4 6.2 + - + +
152A VAL 4.5 0.7 - - - +
153A LEU* 3.3 4.8 - - - -
154A ASP* 2.8 50.3 + - + +
156A TRP* 3.6 28.7 - - + -
164A LEU 4.1 0.2 + - - -
165A LEU* 1.3 80.2 - - - +
167A VAL* 1.3 67.0 + - - +
168A ASP* 5.9 1.7 - - + +
577A GLY 5.5 1.6 - - - +
579A GLY* 4.0 22.2 + - - -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASN* 2.9 32.8 + - - +
14A PHE* 4.1 5.4 - - + -
151A ALA* 3.7 21.8 - - + -
152A VAL 3.6 3.8 - - - -
153A LEU* 3.8 6.7 - - + -
165A LEU* 3.6 20.4 - - + -
166A GLU* 1.3 81.9 - - - +
168A ASP* 1.3 65.3 + - - +
169A PRO* 4.9 0.4 - - + -
290A THR* 3.6 30.8 - - + +
293A ILE* 3.7 16.4 - - + -
294A ALA* 4.0 24.0 - - + -
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASN* 3.8 6.8 + - - +
151A ALA* 3.8 3.6 - - - -
152A VAL* 2.9 41.8 + - + +
166A GLU* 5.9 2.0 - - + +
167A VAL* 1.3 75.7 - - - +
169A PRO* 1.3 74.6 - - - +
170A ALA* 4.1 0.7 - - - +
286A ARG* 3.0 22.1 + - - +
290A THR* 4.7 0.2 + - - -
579A GLY* 6.0 0.3 - - - -
580A ARG* 2.9 47.7 + - - +
582A TYR* 4.5 0.7 + - - -
615A ARG* 4.8 5.0 + - - -
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Residues in contact with PRO 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLY 3.2 13.0 - - - +
151A ALA* 4.0 1.5 - - + -
167A VAL* 4.9 1.1 - - + -
168A ASP* 1.3 97.7 - - - +
170A ALA* 1.3 61.6 + - - +
281A LEU* 3.9 17.7 - - + -
286A ARG* 2.8 44.4 + - + +
289A ARG* 3.9 22.0 - - + +
290A THR* 3.1 32.3 - - - +
293A ILE* 5.0 2.2 - - + -
8C G 5.5 0.3 + - - -
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TYR* 3.3 19.2 - - + +
149A GLY* 3.8 0.9 - - - -
150A GLY 2.9 31.2 + - - +
152A VAL* 4.3 19.1 - - + +
168A ASP 3.6 5.6 + - - +
169A PRO* 1.3 76.7 - - - +
171A TYR* 1.3 66.4 + - - +
286A ARG* 5.5 0.9 - - - +
8C G 3.3 16.6 - - - +
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Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TYR* 3.8 4.6 + - - -
139A HIS* 3.3 42.7 + + + -
147A VAL* 3.9 10.8 - - + -
148A LEU 3.3 5.6 - - - +
149A GLY* 3.7 20.0 - - - -
170A ALA* 1.3 79.6 - - - +
172A ARG* 1.3 62.0 + - - +
278A ALA 4.2 1.7 + - - -
279A LEU* 3.5 49.6 - - + -
281A LEU* 3.5 19.5 - - + +
286A ARG* 6.3 0.2 - - - -
289A ARG* 2.4 35.9 + - - -
8C G 2.6 39.7 + - - +
9C T 3.8 9.4 + - - -
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TRP* 4.9 2.0 - - + +
130A GLU* 2.6 42.4 + - - +
135A TYR* 3.6 41.1 - - + -
146A ARG 3.9 0.2 - - - +
147A VAL* 3.3 4.2 - - - -
148A LEU* 2.8 33.5 + - + +
171A TYR* 1.3 74.8 - - - +
173A ILE* 1.3 75.0 + - - +
174A LEU* 3.8 26.6 + - + +
194A ARG* 3.9 12.4 - - - +
9C T 2.8 32.8 + - - -
10C A 3.2 38.5 + - - -
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Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ARG 3.8 3.6 - - - +
147A VAL* 4.2 17.0 - - + -
172A ARG* 1.3 85.9 + - - +
174A LEU* 1.3 70.5 + - - +
194A ARG* 5.3 2.6 + - - -
265A LEU* 3.9 34.3 + - + +
266A THR 4.3 14.4 - - - +
267A LEU* 3.8 28.7 - - + -
270A LEU* 3.7 29.6 - - + -
279A LEU* 4.5 4.5 - - + -
8C G 3.6 24.0 - - + +
9C T 2.7 13.4 + - - +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TRP* 3.7 51.4 - - + +
145A TRP* 3.3 5.9 - - - +
146A ARG* 2.9 54.9 + - - +
148A LEU* 3.7 26.9 - - + -
172A ARG* 3.8 29.8 - - + +
173A ILE* 1.3 84.7 - - - +
175A CYS* 1.3 63.5 + - - +
176A GLU* 4.7 0.4 - - - +
194A ARG* 5.3 11.4 - - - +
265A LEU* 4.3 4.0 - - - -
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Residues in contact with CYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLY 3.7 13.2 - - - -
174A LEU* 1.3 78.1 - - - +
176A GLU* 1.3 65.7 + - - +
177A MET* 3.5 20.4 - - - -
182A TRP* 4.1 11.7 - - - -
194A ARG* 5.8 3.1 + - - +
262A VAL* 3.9 14.8 - - + +
263A PRO* 3.5 43.2 + - - +
265A LEU* 3.5 22.1 - - + +
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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