Contacts of the strand formed by residues 154 - 165 (chain A) in PDB entry 3HFV
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 ILE 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A VAL* 4.4 10.3 - - + +
37A ARG* 2.8 48.0 - - + +
140A ASP* 4.0 13.9 - - + -
141A VAL 3.4 7.0 - - - +
142A TYR* 3.4 39.0 - - + +
152A TYR* 3.4 25.5 - - + +
153A PRO* 1.3 87.7 - - + +
155A PHE* 1.3 68.1 + - - +
156A HIS* 4.5 0.9 - - + -
281A GLU* 4.1 1.2 - - - +
293A ILE* 5.1 1.0 - - - +
297A TRP* 4.0 27.9 + - + -
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Residues in contact with PHE 155 (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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140A ASP* 3.2 5.5 - - - -
141A VAL* 2.6 62.6 + - + -
143A ARG* 3.6 56.5 - - + -
145A ASP* 6.6 0.2 - - + -
152A TYR 3.6 21.5 - - - -
153A PRO 4.7 2.0 - - - -
154A ILE* 1.3 74.2 - - - +
156A HIS* 1.3 70.6 + - - +
157A GLN* 4.4 12.3 - - + -
279A GLY* 5.6 4.5 - - - -
281A GLU* 2.9 26.0 - - + +
293A ILE* 4.9 5.4 - - + -
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Residues in contact with HIS 156 (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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41A ASN* 5.1 0.4 + - - -
42A LEU* 4.1 15.2 + - + +
43A HIS* 3.5 28.5 + + + -
50A LEU* 3.2 18.8 - - + +
139A GLY 3.2 5.6 - - - +
140A ASP* 3.4 32.2 - - + +
141A VAL 4.5 0.2 - - - +
154A ILE* 4.5 0.7 - - + -
155A PHE* 1.3 82.8 - - - +
157A GLN* 1.3 64.2 + - - +
279A GLY* 3.6 4.3 - - - -
280A LEU* 2.8 45.3 + - + -
281A GLU* 2.7 32.8 + - - +
297A TRP* 3.9 29.8 - + - -
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Residues in contact with GLN 157 (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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119A HIS* 3.0 12.4 - - - +
120A THR* 2.7 48.2 + - + +
137A VAL 3.8 0.5 - - - +
138A VAL* 3.3 6.2 - - - +
139A GLY 3.1 29.6 + - - -
141A VAL* 4.0 13.4 - - + +
143A ARG* 3.7 6.8 - - - +
155A PHE* 4.4 9.0 - - + -
156A HIS* 1.3 78.8 - - - +
158A LEU* 1.3 61.3 + - - +
159A GLU* 4.1 2.7 - - - +
277A GLY* 5.2 4.4 + - - -
278A LEU 3.2 15.4 + - - +
279A GLY* 4.6 4.1 - - - +
280A LEU* 4.2 4.5 - - - -
416A MTY 2.9 30.5 + - - +
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Residues in contact with LEU 158 (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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54A LYS* 4.7 11.2 - - - +
57A VAL* 3.5 42.2 - - + -
58A LYS* 6.0 0.2 - - + -
120A THR* 4.2 2.0 - - - -
136A LEU* 4.3 14.4 - - + -
137A VAL 3.2 3.6 - - - +
138A VAL* 3.7 26.9 - - + +
157A GLN* 1.3 74.5 - - - +
159A GLU* 1.3 76.0 + - - +
276A PHE* 3.9 19.6 - - + +
277A GLY* 3.5 1.6 - - - -
278A LEU* 3.0 47.7 + - + +
280A LEU* 4.2 8.0 - - + +
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Residues in contact with GLU 159 (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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120A THR* 2.6 34.8 + - - +
121A SER* 2.5 38.5 + - - -
124A GLN* 2.8 19.1 + - + +
135A PHE* 5.8 0.4 - - + -
136A LEU* 3.2 6.1 - - - -
137A VAL* 2.6 49.0 + - + +
157A GLN* 4.6 1.6 - - - +
158A LEU* 1.3 81.2 - - - +
160A ALA* 1.3 66.8 + - - +
161A VAL* 4.9 1.8 - - + -
276A PHE 3.4 4.3 - - - +
277A GLY* 3.6 12.0 - - - -
416A MTY 2.6 23.0 + - - +
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Residues in contact with ALA 160 (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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61A PHE* 5.1 0.7 - - + -
74A PHE* 4.7 2.2 - - + -
135A PHE 3.3 6.5 - - - -
136A LEU* 3.6 16.4 - - + -
159A GLU* 1.3 76.2 - - - +
161A VAL* 1.3 63.3 + - - +
274A TRP* 3.8 10.0 - - + -
275A ALA* 3.0 7.8 - - - +
276A PHE* 3.0 65.9 + - + +
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Residues in contact with VAL 161 (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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74A PHE* 3.4 5.9 - - - -
124A GLN* 3.7 28.7 - - + +
128A LEU* 3.6 17.3 - - + -
133A ASP 4.2 1.1 - - - +
134A ALA* 3.2 3.6 - - - -
135A PHE* 3.1 59.8 + - + -
159A GLU* 4.9 2.7 - - + -
160A ALA* 1.3 81.7 - - - +
162A ARG* 1.3 64.7 + - - +
163A LEU* 3.5 24.7 - - + -
258A MET* 3.7 11.7 - - + -
274A TRP* 3.5 4.0 - - - -
275A ALA* 4.2 4.5 - - + -
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Residues in contact with ARG 162 (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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70A GLY* 3.8 11.5 + - - -
71A THR* 4.3 4.2 - - - +
72A PRO* 3.4 35.4 - - + +
74A PHE* 3.6 24.5 - - + -
133A ASP 3.3 3.6 - - - -
134A ALA* 4.4 0.4 - - + +
161A VAL* 1.3 75.3 - - - +
163A LEU* 1.3 83.8 + - - +
164A PHE* 3.2 41.9 - - - -
168A GLU* 3.1 28.5 + - - +
206A ASP* 4.3 5.3 + - - -
273A GLY* 3.0 21.8 - - - -
274A TRP* 3.0 42.3 + - + +
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Residues in contact with LEU 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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128A LEU* 3.8 15.9 - - + +
132A LEU 3.5 17.5 - - - +
133A ASP* 2.7 44.2 + - - +
161A VAL* 3.5 23.6 - - + -
162A ARG* 1.3 108.0 + - - +
164A PHE* 1.3 57.0 + - - +
168A GLU* 4.3 1.9 - - - +
258A MET* 4.2 5.4 - - - -
263A VAL* 5.0 7.0 - - + -
268A ALA* 4.5 12.1 - - + -
271A ARG* 3.8 26.9 + - + -
272A ILE 3.3 4.3 - - - +
273A GLY* 4.1 9.6 - - - +
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Residues in contact with PHE 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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162A ARG* 3.2 46.0 - - - -
163A LEU* 1.3 76.4 - - - +
165A SER* 1.3 64.4 + - - +
168A GLU* 3.9 13.7 - - + -
169A LEU* 3.4 31.6 - - + -
181A LEU* 3.8 2.8 - - - +
203A VAL* 4.3 11.0 - - + -
206A ASP* 3.3 34.8 - - + -
271A ARG* 3.2 10.8 - - - +
272A ILE* 2.5 49.2 + - + +
273A GLY* 4.6 0.9 - - - -
274A TRP* 3.8 21.5 - + - -
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Residues in contact with SER 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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164A PHE* 1.3 76.0 - - - +
166A LYS* 1.3 65.5 + - - +
167A HIS* 3.7 14.5 + - - +
168A GLU* 3.2 32.5 + - - +
169A LEU* 2.9 22.9 + - - +
181A LEU* 4.0 2.2 - - - -
270A ASP 4.0 2.9 - - - -
271A ARG* 3.6 29.8 - - - +
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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