Contacts of the helix formed by residues 162 - 173 (chain B) in PDB entry 3K7G
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 LYS 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B TRP* 3.3 61.0 - - + +
125B VAL* 4.7 3.3 - - + +
155B THR* 4.0 20.4 - - + +
157B ASP* 2.8 28.8 + - - +
159B ASP* 2.8 39.5 + - + +
161B ASN* 1.3 78.4 - - - +
163B TYR* 1.3 59.8 + - + +
164B GLY 3.4 2.0 - - - -
165B LEU* 3.3 9.5 + - - +
166B LEU* 2.9 24.9 + - - +
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Residues in contact with TYR 163 (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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153B ILE 5.1 0.2 - - - -
154B THR* 3.3 17.9 - - + +
155B THR* 3.6 27.4 - - - -
158B ARG* 3.3 28.2 + - - +
159B ASP 3.2 17.5 - - - -
160B ARG* 3.3 25.0 + - + +
161B ASN 3.3 0.2 - - - -
162B LYS* 1.3 78.5 - - + +
164B GLY* 1.3 61.4 + - - +
166B LEU* 3.5 11.6 - - + +
167B ALA* 2.9 24.9 + - - +
180B TYR* 3.9 15.9 - + + +
183B LYS 3.3 24.2 - - - -
184B ALA 3.4 26.1 + - - -
185B HIS* 3.9 6.7 - - - -
186B VAL* 3.5 16.7 - - + +
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Residues in contact with GLY 164 (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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46B PRO* 3.4 10.0 - - - +
47B LEU 3.0 39.1 + - - -
160B ARG 4.9 0.2 + - - -
161B ASN 4.6 3.2 + - - -
162B LYS 3.4 0.8 - - - -
163B TYR* 1.3 76.6 - - - +
165B LEU* 1.3 61.0 + - - +
167B ALA* 3.4 2.8 + - - +
168B ARG 3.2 11.8 + - - -
180B TYR* 3.6 17.4 + - - -
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.4 22.4 - - + +
46B PRO* 3.5 18.4 - - + +
121B GLN* 3.6 37.2 - - - +
122B TRP* 3.8 19.5 - - + +
161B ASN 5.3 1.0 + - - +
162B LYS* 3.3 10.3 + - - +
164B GLY* 1.3 74.6 - - - +
166B LEU* 1.3 65.0 + - - +
168B ARG* 3.0 12.1 + - + -
169B LEU* 2.9 26.6 + - + +
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 4.6 2.7 - - + -
118B VAL* 3.6 31.2 - - + -
122B TRP* 3.8 16.3 - - + -
127B LEU* 4.2 4.7 - - + -
153B ILE* 3.7 31.2 - - + +
154B THR* 3.5 37.0 - - - +
155B THR* 3.9 7.6 - - + +
162B LYS 2.9 15.9 + - - +
163B TYR* 3.5 15.0 - - + +
165B LEU* 1.3 75.1 - - - +
167B ALA* 1.3 58.9 + - - +
169B LEU* 3.2 6.5 + - + +
170B ALA* 2.9 26.3 + - - +
186B VAL* 4.4 4.7 - - + -
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Residues in contact with ALA 167 (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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47B LEU* 3.9 21.5 - - + -
163B TYR 2.9 13.8 + - - +
164B GLY* 3.5 10.5 - - - +
166B LEU* 1.3 77.3 - - - +
168B ARG* 1.3 62.7 + - - +
170B ALA* 3.1 6.1 + - - +
171B VAL* 3.1 18.9 + - - +
178B VAL* 3.5 13.5 - - + +
180B TYR* 4.7 4.7 - - + -
186B VAL* 3.7 30.9 - - + +
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Residues in contact with ARG 168 (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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1B SO4 2.9 42.8 + - - -
44B LEU* 4.1 26.7 - - + -
45B VAL* 2.8 41.2 + - - +
46B PRO* 4.2 4.5 + - + -
47B LEU* 3.6 24.1 - - + +
51B GLN* 4.2 5.9 - - - +
53B SER* 4.2 0.2 + - - -
164B GLY 3.2 8.2 + - - +
165B LEU* 3.0 11.7 + - + +
167B ALA* 1.3 79.0 - - - +
169B LEU* 1.3 62.9 + - - +
171B VAL* 3.2 22.9 + - - +
172B GLU* 3.0 32.7 + - - +
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Residues in contact with LEU 169 (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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44B LEU* 4.2 18.8 - - + -
114B LEU* 3.6 13.9 - - + +
117B SER* 4.1 22.2 - - - +
118B VAL* 4.4 8.3 - - + -
121B GLN* 3.7 44.6 - - + +
122B TRP* 3.8 22.9 - - + -
165B LEU* 2.9 17.1 + - + +
166B LEU* 3.2 7.2 + - - +
168B ARG* 1.3 76.5 - - - +
170B ALA* 1.3 57.0 + - - +
172B GLU* 3.1 10.5 + - + +
173B ALA* 2.8 29.5 + - - +
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Residues in contact with ALA 170 (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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114B LEU* 3.6 21.4 - - + +
153B ILE* 4.5 1.1 - - + -
166B LEU 2.9 13.5 + - - +
167B ALA* 3.1 9.4 + - - +
169B LEU* 1.3 77.0 - - - +
171B VAL* 1.3 61.1 + - - +
173B ALA* 3.4 5.4 + - - -
174B GLY 3.4 0.5 + - - -
175B PHE* 3.2 28.5 + - + +
178B VAL* 3.8 9.4 - - + -
188B CYS* 3.7 30.1 - - - -
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Residues in contact with VAL 171 (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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1B SO4 4.6 1.1 - - - +
47B LEU* 4.3 4.9 - - + -
53B SER* 3.8 32.5 - - - +
54B PRO* 6.3 0.7 - - + -
167B ALA 3.1 14.5 + - - +
168B ARG* 3.2 29.1 + - - +
170B ALA* 1.3 76.2 - - - +
172B GLU* 1.3 66.6 + - - +
174B GLY* 3.0 15.9 + - - -
175B PHE 4.2 6.8 + - - +
178B VAL* 3.8 20.6 - - + -
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 2.9 32.1 + - - -
44B LEU* 4.1 26.5 - - + +
117B SER* 6.6 0.2 - - - -
168B ARG* 3.0 26.4 + - - +
169B LEU* 3.6 13.7 - - + +
171B VAL* 1.3 81.0 - - - +
173B ALA* 1.3 59.9 + - - +
174B GLY* 3.2 1.6 + - - -
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Residues in contact with ALA 173 (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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110B ARG* 2.8 35.3 + - - +
113B SER* 3.9 9.7 + - - +
114B LEU* 3.7 38.6 - - + +
117B SER* 5.4 4.5 - - - +
169B LEU 2.8 16.0 + - - +
170B ALA 3.7 7.0 - - - +
171B VAL 3.1 0.6 - - - -
172B GLU* 1.3 77.2 - - - +
174B GLY* 1.3 57.0 + - - +
175B PHE* 3.6 2.2 - - + -
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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