Contacts of the strand formed by residues 173 - 181 (chain I) in PDB entry 2NX5
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 173 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I ASN 6.2 0.2 - - - -
143I ASP* 4.3 6.1 - - - -
166I LEU* 5.2 0.2 - - + -
167I ASP* 2.9 9.1 + - - +
168I MET* 2.7 57.9 + - + +
171I MET* 4.1 13.5 - - + +
172I ASP* 1.3 78.0 - - - +
174I LYS* 1.3 71.7 + - - +
175I SER* 3.6 30.7 - - - -
143J LYS* 3.6 39.0 - - + -
198J ARG* 3.7 14.1 - - - -
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Residues in contact with LYS 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I GLU* 3.1 37.7 + - - +
82I MET* 3.9 24.0 - - + +
116I PRO* 4.2 17.9 - - + -
117I TYR 5.4 3.5 - - - +
118I ILE* 3.6 17.0 - - + +
165I VAL* 4.6 4.9 - - + -
166I LEU 3.4 9.2 - - - +
167I ASP* 3.3 34.9 + - + +
172I ASP* 4.5 9.0 + - - -
173I PHE* 1.3 85.7 - - - +
175I SER* 1.3 62.5 + - - +
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Residues in contact with SER 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I ILE* 4.4 6.1 - - - -
142I THR* 4.9 0.2 + - - -
143I ASP* 4.0 8.1 - - - +
164I CYS 3.6 0.3 - - - +
165I VAL* 3.4 8.7 - - - +
166I LEU* 3.1 52.6 + - - +
173I PHE* 3.6 11.9 - - - -
174I LYS* 1.3 75.5 - - - +
176I ASN* 1.3 67.6 + - - +
177I SER* 5.8 0.2 - - - -
198J ARG* 3.1 30.2 + - - -
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Residues in contact with ASN 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I HIS* 5.9 1.0 - - - -
116I PRO* 4.0 5.8 - - - +
118I ILE* 3.4 22.6 - - - +
142I THR* 3.0 19.4 + - - -
143I ASP* 3.1 12.8 + - - +
144I PHE* 3.0 53.7 + - + +
145I ASP 3.8 0.2 - - - -
146I SER* 3.5 18.8 + - - +
163I LYS* 5.1 8.7 - - + +
164I CYS 3.5 5.4 - - - +
165I VAL* 3.4 22.9 - - - +
175I SER* 1.3 75.8 - - - +
177I SER* 1.3 60.7 + - - +
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Residues in contact with SER 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I LEU* 3.9 12.3 - - - -
141I PHE 3.2 5.8 - - - -
142I THR* 3.8 11.0 - - - -
144I PHE* 3.8 4.9 - - - -
164I CYS 3.1 27.3 + - - +
166I LEU* 4.0 12.6 - - - +
175I SER* 5.8 0.2 - - - -
176I ASN* 1.3 79.1 - - - +
178I ALA* 1.3 59.4 + - - +
145J THR* 6.1 0.9 - - - -
174J CYS* 3.9 2.8 - - - -
196J ARG* 2.9 50.1 + - - -
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Residues in contact with ALA 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I LEU* 3.3 8.7 - - - +
141I PHE* 2.7 35.6 + - + +
144I PHE* 4.1 1.3 - - + -
150I VAL* 3.8 24.5 - - + -
161I THR* 3.9 13.0 - - - +
162I ASP 4.6 2.2 - - - +
163I LYS* 4.8 0.4 - - - -
177I SER* 1.3 74.3 - - - +
179I VAL* 1.3 62.1 + - - +
193I PHE* 3.8 24.0 - - + -
196J ARG* 3.5 4.0 - - - +
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Residues in contact with VAL 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I VAL* 3.5 21.5 - - + -
139I CYS 3.6 3.4 - - - +
140I LEU* 3.8 14.1 - - + -
159I TYR 3.6 1.0 - - - +
160I ILE* 3.4 2.6 - - - -
161I THR* 3.0 40.1 + - + +
178I ALA* 1.3 79.8 - - - +
180I ALA* 1.3 62.6 + - - +
181I TRP* 3.9 17.0 - - + -
193I PHE* 4.2 1.3 - - - -
147J VAL* 4.1 20.2 - - + -
149J LEU* 4.4 1.8 - - + -
194J SER* 4.0 17.7 - - - +
196J ARG* 3.7 22.9 - - + +
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Residues in contact with ALA 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I VAL* 3.7 1.1 - - - -
139I CYS* 2.8 42.5 + - + +
158I VAL* 4.9 1.8 - - + -
159I TYR 3.2 7.9 - - - +
160I ILE* 4.3 12.8 - - + -
179I VAL* 1.3 75.0 - - - +
181I TRP* 1.3 62.8 + - - +
187I PHE* 4.4 5.4 - - + -
192I ALA* 4.6 13.5 - - + +
193I PHE* 3.6 29.5 - - + -
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Residues in contact with TRP 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I SER 3.8 8.5 - - - +
138I VAL* 3.7 18.8 - - + -
159I TYR* 2.7 90.3 + + + -
161I THR* 3.8 21.5 - - + -
179I VAL* 3.9 10.3 - - + -
180I ALA* 1.3 74.7 - - - +
182I SER* 1.3 65.1 + - - +
183I ASN* 4.9 5.1 - - - +
187I PHE* 3.8 10.5 - - - -
149J LEU* 3.6 44.7 - - + +
151J THR* 4.0 10.3 - - + +
180J LEU* 4.0 20.2 - - + -
182J GLU* 5.2 0.6 + - - -
192J ALA* 3.7 22.9 - - + -
193J LEU 5.1 0.2 - - - -
194J SER* 5.3 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