Contacts of the helix formed by residues 115 - 130 (chain B) in PDB entry 4F56
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 ASN 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ALA* 3.8 8.3 - - - -
61B VAL 2.8 25.0 + - - +
62B SER* 3.8 1.8 - - - +
64B GLU* 3.7 30.4 - - + +
65B SER* 2.9 33.6 + - - +
114B PRO* 1.3 73.5 - - - +
116B ALA* 1.3 58.7 + - - +
117B GLY* 2.8 27.9 + - - -
118B HIS* 3.0 17.7 + - - -
119B ARG* 3.0 29.8 + - - +
293B CYS* 5.7 0.6 - - - -
294B GLY* 5.0 1.0 - - - -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A PRO* 3.6 41.7 - - + +
299A GLU* 3.9 7.3 - - + +
302A ALA* 3.8 5.6 - - - +
115B ASN* 1.3 75.0 - - - +
117B GLY* 1.3 57.3 + - - +
119B ARG* 3.8 4.7 - - - +
120B ALA* 2.9 31.5 + - - +
294B GLY* 3.5 24.2 - - - +
298B PRO* 3.9 4.3 - - + +
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Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 4.6 4.5 - - - -
115B ASN* 2.8 9.8 + - - -
116B ALA* 1.3 75.8 - - - +
118B HIS* 1.3 63.4 + - - -
120B ALA* 3.4 2.4 + - - +
121B ILE* 3.1 30.3 + - - +
293B CYS* 4.1 11.4 - - - -
294B GLY* 3.8 6.7 - - - -
297B LEU* 3.9 23.7 - - - +
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Residues in contact with HIS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.4 12.8 + - + +
62B SER* 2.9 28.6 + - - -
65B SER* 3.4 10.5 - - - -
114B PRO* 3.5 6.8 - - + +
115B ASN* 3.0 48.8 + - - +
117B GLY* 1.3 73.4 - - - +
119B ARG* 1.3 62.8 + - - +
121B ILE* 3.4 7.8 + - - +
122B ALA* 3.0 18.4 + - - +
141B ASN* 5.2 0.2 + - - -
143B ASP* 5.0 0.2 + - - -
145B LEU* 3.6 25.2 - - + +
146B HIS* 3.8 29.6 + + - +
149B ALA* 3.5 25.5 - - + +
151B THR* 4.8 1.2 + - - -
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 3.3 39.1 - - - +
298A PRO 6.0 0.2 - - - +
302A ALA* 2.8 36.6 + - + +
114B PRO* 4.0 20.6 - - + +
115B ASN 3.0 20.8 + - - +
116B ALA* 3.8 6.7 - - - +
117B GLY 3.2 0.2 - - - -
118B HIS* 1.3 74.0 - - - +
120B ALA* 1.3 57.0 + - - +
122B ALA* 3.2 2.6 + - - +
123B GLU* 2.8 60.1 + - - +
148B LYS 3.7 5.7 + - - -
149B ALA* 3.1 35.7 + - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA 2.9 19.0 + - - +
117B GLY 3.7 4.5 - - - +
118B HIS 3.4 0.2 - - - -
119B ARG* 1.3 75.3 - - - +
121B ILE* 1.3 57.7 + - - +
123B GLU* 3.9 10.1 + - - +
124B CYS* 2.9 33.1 + - - +
297B LEU* 4.1 10.1 - - + +
298B PRO* 3.9 32.3 - - + -
301B LEU* 4.0 8.9 - - + +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 4.0 29.8 - - + -
57B SER* 5.4 0.7 - - - -
61B VAL* 4.0 10.1 - - + -
117B GLY 3.1 17.7 + - - +
118B HIS* 3.7 4.9 - - - +
120B ALA* 1.3 76.2 - - - +
122B ALA* 1.3 62.3 + - - +
124B CYS* 3.5 3.1 + - - +
125B GLU* 3.2 20.8 + - - +
135B VAL* 4.7 2.9 - - - +
137B VAL* 3.4 32.8 - - + -
146B HIS* 3.9 23.3 - - + +
151B THR* 4.1 5.8 - - - +
248B VAL* 4.9 2.5 - - + -
297B LEU* 3.7 23.8 - - + -
301B LEU* 4.2 14.8 - - + -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B HIS 3.0 16.0 + - - +
119B ARG* 3.2 3.8 + - - +
121B ILE* 1.3 77.6 - - - +
123B GLU* 1.3 58.2 + - + +
125B GLU* 3.2 7.9 + - - +
126B THR* 3.1 30.0 + - - -
149B ALA* 3.3 27.1 - - + +
150B GLY* 3.7 4.5 - - - +
151B THR* 3.6 30.5 + - - +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 1.4 70.5 - - + +
127A ARG* 4.2 7.8 + - - -
119B ARG* 2.8 49.2 + - - +
120B ALA* 4.0 8.0 + - - +
122B ALA* 1.3 70.9 - - + +
124B CYS* 1.3 65.9 + - - +
126B THR* 3.4 7.1 + - - +
127B ARG* 3.0 30.2 + - - +
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Residues in contact with CYS 124 (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 PHE* 3.7 35.4 - - - -
53B ILE* 4.8 1.6 - - - -
55B ILE* 5.2 1.8 - - - -
120B ALA 2.9 19.6 + - - +
121B ILE* 3.6 5.4 - - - +
122B ALA 3.3 0.2 - - - -
123B GLU* 1.3 76.4 - - - +
125B GLU* 1.3 56.6 + - - +
127B ARG* 4.3 12.0 - - - +
128B LEU* 2.9 34.3 + - - +
135B VAL* 4.0 20.2 - - - -
301B LEU* 4.2 23.8 - - + +
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Residues in contact with GLU 125 (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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121B ILE 3.2 8.8 + - - +
122B ALA 3.2 7.9 + - - +
124B CYS* 1.3 78.0 - - - +
126B THR* 1.3 58.5 + - - +
128B LEU* 4.0 0.5 - - - +
129B GLY* 2.9 29.3 + - - -
133B ARG 4.8 0.5 - - - +
135B VAL* 3.7 35.9 + - + +
137B VAL* 5.2 2.4 - - + +
151B THR* 3.3 20.1 + - - +
152B LYS* 3.0 36.3 + - - +
153B ASN* 2.7 42.3 + - - +
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Residues in contact with THR 126 (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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130A LYS* 6.1 2.5 - - - +
122B ALA 3.1 16.6 + - - -
123B GLU* 3.8 8.0 - - - -
124B CYS 3.4 0.2 - - - -
125B GLU* 1.3 78.2 - - - +
127B ARG* 1.3 63.1 + - - +
129B GLY* 3.4 2.2 + - - -
130B LYS* 3.4 45.5 + - - +
150B GLY 4.8 1.6 + - - -
152B LYS* 3.4 31.1 + - - +
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 3.5 39.3 - - - +
123A GLU* 4.1 15.2 + - - -
47B PHE* 3.8 15.2 - - - -
123B GLU* 3.0 26.8 + - - +
124B CYS* 4.0 8.6 - - - +
126B THR* 1.3 77.0 - - - +
128B LEU* 1.3 74.2 + - + +
130B LYS* 3.4 18.7 + - - +
131B GLN* 3.7 17.6 + - - +
301B LEU 2.6 29.7 + - - -
302B ALA* 3.7 15.8 + - - +
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Residues in contact with LEU 128 (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 PHE* 4.4 6.5 - - + -
50B ALA 4.6 0.4 - - - +
51B LYS 6.3 0.2 - - - -
53B ILE* 3.6 32.1 - - + -
124B CYS* 2.9 28.9 + - - +
127B ARG* 1.3 95.1 - - - +
129B GLY* 1.3 63.1 + - - +
131B GLN* 2.9 18.7 + - - +
133B ARG* 2.9 78.0 + - + +
134B ARG 5.1 0.7 - - - +
135B VAL* 3.7 16.4 - - + -
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Residues in contact with GLY 129 (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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125B GLU 2.9 16.9 + - - -
126B THR* 3.8 3.1 - - - -
127B ARG 3.3 0.4 - - - -
128B LEU* 1.3 75.4 - - - +
130B LYS* 1.3 57.4 + - - +
132B GLY* 2.9 19.3 + - - -
133B ARG 3.3 11.0 + - - -
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Residues in contact with LYS 130 (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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126A THR* 6.2 1.6 - - - +
126B THR* 3.4 34.5 + - - +
127B ARG* 3.4 11.7 + - - +
128B LEU 3.2 0.8 - - - -
129B GLY* 1.3 76.7 - - - +
131B GLN* 1.3 58.9 + - + +
132B GLY 3.3 0.9 - - - -
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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