Contacts of the helix formed by residues 134 - 148 (chain B) in PDB entry 4K9N
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 GLU 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B TYR* 2.5 38.4 + - - -
129B PRO* 4.0 3.6 - - + -
130B ALA* 2.9 32.9 + - - +
131B SER* 3.3 19.9 + - - +
132B ALA 3.1 0.8 - - - -
133B ALA* 1.3 78.3 - - - +
135B VAL* 1.3 64.2 + - - +
136B PRO 3.4 0.7 - - - -
137B HIS* 3.0 17.6 + - + +
138B ALA* 2.9 21.8 + - + +
141B ARG* 4.3 0.9 + - - -
101C ARG 4.6 5.9 - - - +
104C ILE* 4.7 0.6 - - - +
105C GLY* 3.1 30.8 + - - +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 3.7 16.2 - - + -
8B THR* 4.1 4.7 - - + +
129B PRO* 4.0 17.3 - - + -
131B SER 4.0 4.7 - - - +
132B ALA 3.0 18.0 + - - +
134B GLU* 1.3 76.7 - - - +
136B PRO* 1.3 67.2 - - + +
138B ALA* 3.2 2.4 + - - +
139B MET* 2.9 22.2 + - + +
156B LEU* 4.7 3.9 - - + +
158B VAL* 3.9 20.2 - - + -
162B ASP* 3.5 26.9 - - + +
163B TRP* 4.0 24.2 - - + -
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Residues in contact with PRO 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 4.1 10.8 - - + -
7B THR* 3.9 32.5 - - + -
8B THR* 3.9 20.9 - - - +
11B LEU* 3.4 13.9 - - + +
132B ALA 4.0 2.2 - - - +
133B ALA* 3.4 16.6 - - - +
135B VAL* 1.3 94.9 - - + +
137B HIS* 1.3 56.8 + - - +
139B MET* 3.3 4.7 + - + -
140B SER 3.0 23.2 + - - -
167B ALA* 4.7 4.0 - - + -
171B SER* 4.1 8.3 - - - +
174B LEU* 3.5 14.1 - - + +
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Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A TYR* 6.1 1.1 - - - -
306A ALA 5.3 0.2 - - - -
307A ARG* 2.7 31.2 + - - -
308A ALA 4.5 1.6 - - - -
309A PRO* 4.2 13.7 - - + +
133B ALA 4.9 2.2 + - - +
134B GLU* 3.0 17.3 + - + +
136B PRO* 1.3 80.4 - - - +
138B ALA* 1.3 61.5 + - - +
140B SER* 3.2 5.7 + - - -
141B ARG* 3.0 31.6 + - + +
171B SER* 5.0 1.9 + - - +
174B LEU* 3.6 31.7 - - + +
105C GLY* 3.2 43.6 - - - -
106C VAL* 3.8 5.4 - - + -
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B TRP* 3.7 4.2 - - - -
127B TYR* 4.0 16.8 - - + -
129B PRO* 3.9 13.9 - - + -
134B GLU* 2.9 13.6 + - + +
135B VAL 3.6 6.3 - - - +
137B HIS* 1.3 77.5 + - - +
139B MET* 1.3 58.9 + - - +
141B ARG* 3.3 13.5 + - - +
142B ALA* 3.0 26.7 + - - +
156B LEU* 3.8 25.0 - - + +
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Residues in contact with MET 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 3.8 27.1 - - + -
11B LEU* 4.0 13.9 - - + -
12B LEU* 4.2 12.1 - - + -
31B PHE* 5.2 0.2 - - + -
66B PHE* 3.7 29.2 - - + -
93B ILE* 4.4 8.5 - - - -
95B THR* 4.0 17.7 - - + -
135B VAL* 2.9 16.9 + - + +
136B PRO* 3.6 7.9 - - + +
138B ALA* 1.3 76.1 - - - +
140B SER* 1.3 63.6 + - - +
142B ALA* 3.2 3.6 + - - +
143B ILE* 3.0 28.9 + - + +
156B LEU* 3.9 24.4 - - + +
158B VAL* 5.5 0.4 - - + -
163B TRP* 4.4 14.6 - - + -
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ALA 4.5 1.8 + - - -
308A ALA 5.0 0.3 + - - -
11B LEU* 3.6 16.0 - - - +
136B PRO 3.0 13.1 + - - -
137B HIS* 3.2 10.3 + - - -
139B MET* 1.3 77.4 - - - +
141B ARG* 1.3 62.3 + - - +
143B ILE* 3.3 7.1 + - - +
144B HIS* 3.0 46.1 + - - -
174B LEU* 3.8 30.4 + - - +
177B ARG* 4.3 8.5 + - - -
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 5.6 4.6 + - - +
306A ALA* 3.4 29.1 - - + +
307A ARG* 3.6 16.9 - - - +
125B TRP* 3.5 46.0 - - + +
127B TYR* 4.0 19.2 - - - -
134B GLU* 4.3 0.4 + - - -
137B HIS* 3.0 34.9 + - + +
138B ALA* 3.4 10.3 - - - +
140B SER* 1.3 76.1 - - - +
142B ALA* 1.3 57.0 + - - +
144B HIS* 3.3 0.9 + - - -
145B MET* 2.8 36.0 + - + +
104C ILE 4.9 1.2 + - - -
105C GLY* 3.1 30.3 + - - -
107C GLU* 3.0 28.3 + - - +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 4.2 14.4 - - + -
125B TRP* 3.7 16.7 - - + -
138B ALA 3.0 13.4 + - - +
139B MET* 3.2 12.3 + - - +
141B ARG* 1.3 76.1 - - - +
143B ILE* 1.3 62.9 + - - +
145B MET* 3.9 0.6 - - - +
146B ALA* 3.0 26.5 + - - +
154B VAL* 3.5 22.8 - - + +
156B LEU* 4.8 12.1 - - + -
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Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.0 28.0 - - + -
12B LEU* 4.2 17.3 - - + -
15B GLN* 4.1 37.5 - - + +
17B ILE* 4.2 6.7 - - + -
64B PRO* 5.3 4.0 - - + -
93B ILE* 3.9 26.0 - - + +
139B MET* 3.0 24.2 + - + +
140B SER* 3.3 7.6 + - - +
142B ALA* 1.3 75.4 - - - +
144B HIS* 1.3 68.5 + - + +
146B ALA* 3.4 2.4 + - - +
147B SER* 2.8 34.6 + - - +
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Residues in contact with HIS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ALA* 4.2 16.4 - - - -
11B LEU* 6.1 0.4 - - - +
15B GLN* 3.5 28.3 + - - -
140B SER* 3.0 40.5 + - - +
141B ARG 4.1 1.6 - - - +
143B ILE* 1.3 81.7 - - + +
145B MET* 1.3 65.2 + - - +
147B SER* 4.3 6.0 - - - -
148B MET* 2.9 36.8 + - + +
174B LEU 5.2 0.4 + - - -
177B ARG* 3.8 37.6 - - - +
179B VAL* 3.5 33.8 + - + +
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Residues in contact with MET 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PRO* 3.9 9.4 - - + +
303A LEU* 3.8 29.8 - - + -
306A ALA* 3.6 22.9 - - + -
124B LYS* 2.8 69.8 + - - +
125B TRP* 4.1 20.6 - - + -
141B ARG* 2.8 26.5 + - + +
142B ALA* 4.0 0.4 - - - +
144B HIS* 1.3 73.5 - - - +
146B ALA* 1.3 58.8 + - - +
147B SER 3.5 0.2 + - - -
148B MET* 3.6 12.7 + - - -
154B VAL* 3.9 17.0 - - + -
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Residues in contact with ALA 146 (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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64B PRO* 5.2 0.4 - - + -
91B PRO* 3.5 14.6 - - + +
92B LEU 4.0 14.4 - - - +
93B ILE* 4.0 13.0 - - + -
142B ALA 3.0 17.7 + - - +
143B ILE 3.8 4.3 - - - +
145B MET* 1.3 78.2 - - - +
147B SER* 1.3 58.8 + - - +
151B GLN* 3.4 11.6 - - - +
152B GLY 3.3 41.2 + - - +
154B VAL* 3.7 4.8 - - + +
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PRO* 3.6 26.3 - - - +
91B PRO* 4.6 1.3 - - - -
143B ILE* 2.8 23.7 + - - +
144B HIS* 3.2 10.3 + - - -
146B ALA* 1.3 76.5 - - - +
148B MET* 1.3 63.9 + - - +
149B ALA 3.7 0.9 + - - -
151B GLN* 2.9 28.9 + - - +
181B SER* 4.6 1.6 + - - -
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Residues in contact with MET 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PRO* 3.2 37.9 - - + +
305A ALA* 3.9 2.2 - - - -
306A ALA* 3.9 6.3 - - + +
315A VAL* 3.8 21.5 - - + -
124B LYS* 2.9 25.1 + - - +
144B HIS* 2.9 26.3 + - + +
145B MET* 3.6 22.0 - - + -
146B ALA 3.6 0.4 - - - -
147B SER* 1.3 79.1 - - - +
149B ALA* 1.3 65.8 + - - +
150B PRO 3.1 7.2 - - - -
151B GLN* 3.2 3.3 + - - -
179B VAL* 3.6 35.4 - - + +
181B SER* 3.8 11.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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