Contacts of the strand formed by residues 176 - 185 (chain C) in PDB entry 4NZD
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 SER 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C ASN* 3.6 6.4 + - - +
144C ARG* 3.0 51.9 + - - +
145C GLY 4.6 1.0 + - - +
175C SER* 1.3 74.8 - - - +
177C TYR* 1.3 60.1 + - - +
203C ILE* 3.7 14.9 - - - +
204C PHE 3.7 4.2 + - - -
205C GLN* 3.4 17.1 + - - +
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Residues in contact with TYR 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C TYR* 4.4 10.5 - + + -
142C ARG* 3.3 23.1 - - - -
143C ASN* 3.8 26.8 + - + +
144C ARG* 4.1 2.5 - - - -
153C ARG* 5.8 3.2 + - - -
170C GLU 4.6 2.5 + - - -
171C PHE* 3.7 26.1 - + + -
172C ARG* 3.0 41.0 + - - +
175C SER* 3.8 20.2 - - - -
176C SER* 1.3 78.8 - - - +
178C GLU* 1.3 59.3 + - - +
202C VAL 3.9 0.3 - - - +
203C ILE* 3.5 10.4 - - - +
204C PHE* 3.1 53.6 + - + -
206C THR* 3.7 17.3 - - + -
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Residues in contact with GLU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C GLN 4.0 0.2 - - - +
141C TYR* 3.0 6.8 - - - +
142C ARG* 2.9 78.9 + - + +
144C ARG* 4.0 24.3 + - - +
177C TYR* 1.3 73.6 - - - +
179C LEU* 1.3 63.9 + - - +
201C PRO* 4.2 26.8 - - + +
202C VAL 3.7 2.5 - - - +
203C ILE* 4.3 18.7 - - + +
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C VAL* 3.7 27.2 - - + +
109C VAL* 4.9 2.5 - - + -
117C ILE* 4.1 28.9 - - + -
139C LEU* 4.6 10.3 - - + -
140C GLN 3.3 10.5 - - - +
141C TYR* 3.9 26.2 - - + -
171C PHE* 4.6 13.2 - - + -
178C GLU* 1.3 77.8 - - - +
180C GLN* 1.3 68.1 + - - +
181C VAL* 4.1 9.6 - - + -
200C ASP 4.5 0.5 - - - +
201C PRO* 3.3 4.7 - - - +
202C VAL* 2.9 42.0 + - + +
204C PHE* 4.3 15.3 - - + -
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Residues in contact with GLN 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C VAL* 5.1 0.4 - - - -
138C GLU 3.9 0.2 - - - +
139C LEU* 3.6 3.6 - - - -
140C GLN* 2.9 63.2 + - - +
179C LEU* 1.3 79.2 - - - +
181C VAL* 1.3 65.6 + - - +
198C TRP* 3.4 32.4 - - + +
199C SER* 2.9 34.0 + - - +
201C PRO* 4.2 18.3 - - + +
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PRO* 3.8 16.8 - - + +
107C VAL* 3.9 24.9 - - + -
119C TRP* 3.8 39.9 - - + -
137C TYR* 4.3 4.0 - - + -
138C GLU 3.4 10.3 - - - +
139C LEU* 3.6 21.5 - - + -
179C LEU* 4.1 2.2 - - + -
180C GLN* 1.3 80.7 - - - +
182C ARG* 1.3 71.2 + - - +
198C TRP* 3.7 2.9 - - - -
199C SER* 2.9 35.0 + - - +
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Residues in contact with ARG 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PRO* 3.9 6.1 - - - -
137C TYR* 3.2 8.5 - - - +
138C GLU* 2.6 64.2 + - + -
154C ARG* 3.5 21.8 - - - +
181C VAL* 1.3 75.0 - - - +
183C ALA* 1.3 60.4 + - - +
195C TRP* 3.5 46.1 - - + +
196C SER* 3.7 18.7 + - - +
197C GLU 3.9 7.0 - - - +
198C TRP* 3.4 42.9 - - + +
301C MAN 3.2 33.5 + - - -
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PRO* 3.5 19.9 - - + +
102C ALA 4.3 3.4 - - - +
104C PRO* 3.9 9.6 - - + +
123C TYR* 6.3 0.2 - - + -
135C LEU* 4.8 6.3 - - + -
136C GLN 3.5 4.7 - - - +
137C TYR* 3.5 26.0 - - + -
182C ARG* 1.3 75.0 - - - +
184C GLY* 1.3 57.0 + - - +
195C TRP* 3.4 5.6 - - - -
196C SER* 2.7 44.5 + - - +
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Residues in contact with GLY 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PRO* 3.6 9.2 - - - +
135C LEU* 3.6 5.2 - - - +
136C GLN* 3.0 36.0 + - - +
183C ALA* 1.3 76.3 - - - +
185C PRO* 1.3 74.2 - - - +
194C THR 4.3 2.5 - - - -
195C TRP* 3.5 15.7 - - - -
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Residues in contact with PRO 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ILE* 3.9 12.8 - - + +
101C PRO* 4.2 5.8 - - + -
134C LYS 4.0 6.3 - - - +
135C LEU* 4.4 6.1 - - + -
136C GLN* 3.9 6.9 + - - -
184C GLY* 1.3 82.6 - - - +
186C MET* 1.3 61.3 + - - +
187C PRO* 3.8 6.4 - - - +
191C TYR* 3.7 27.9 - - + +
192C GLN* 3.5 8.7 - - - +
193C GLY* 3.4 29.8 - - - +
194C THR 3.5 19.5 - - - +
309C CL 4.1 14.2 - - + +
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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