Contacts of the helix formed by residues 119 - 135 (chain A) in PDB entry 3M4A
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 PRO 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ALA* 3.9 14.6 - - + -
116A SER 3.2 18.6 - - - +
117A GLY 3.4 3.6 - - - +
118A LEU* 1.4 93.0 - - - +
120A PRO* 1.3 77.6 - - + +
121A ARG* 4.7 2.7 - - + +
122A LYS* 3.1 30.7 + - + +
123A VAL* 3.1 11.4 + - - +
206A THR* 3.2 1.3 - - - +
207A VAL 4.2 7.1 - - - +
117E T 6.4 0.2 - - - -
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Residues in contact with PRO 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PRO* 1.3 88.9 - - + +
121A ARG* 1.3 60.1 + - + +
123A VAL* 3.3 2.4 + - - +
124A MET* 2.9 39.2 + - + +
206A THR* 3.1 19.5 - - + +
207A VAL 5.5 0.7 - - - +
208A ASP* 6.1 2.7 - - - +
215A ARG* 3.5 29.2 - - - +
217A ILE* 4.3 4.8 - - + +
221A GLU* 4.0 9.4 - - - +
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 5.4 6.7 - - - -
108A ALA* 5.5 2.8 + - - +
112A ASP* 2.9 49.4 + - + +
119A PRO* 3.4 2.3 - - + +
120A PRO* 1.3 79.8 - - + +
122A LYS* 1.3 56.7 + - - +
124A MET* 4.0 17.4 - - + +
125A ALA* 2.9 29.8 + - - +
225A TYR* 3.9 16.2 + - + -
228A GLU* 2.9 43.0 + - - -
229A VAL* 4.9 3.2 - - - +
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Residues in contact with LYS 122 (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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112A ASP 3.5 20.0 + - - +
113A LEU* 2.8 31.4 + - + +
115A ALA 3.0 25.8 + - - +
117A GLY 3.5 18.2 + - - +
118A LEU* 4.9 3.4 - - + -
119A PRO* 3.1 23.7 + - + +
121A ARG* 1.3 76.4 - - - +
123A VAL* 1.3 59.5 + - - +
125A ALA* 3.2 3.3 + - - +
126A LEU* 2.9 38.3 + - + +
191A ASN* 3.4 26.8 + - - +
194A LYS* 4.2 1.8 - - - +
9D G 4.0 9.1 - - - -
10D G 2.7 24.7 + - - -
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.8 28.7 - - + +
119A PRO 3.1 13.8 + - - +
120A PRO 3.9 5.6 - - - +
122A LYS* 1.3 75.2 - - - +
124A MET* 1.3 59.0 + - - +
126A LEU* 3.2 9.7 + - + +
127A MET* 2.9 35.7 + - - +
195A LEU* 4.4 7.2 - - + -
204A PHE* 4.2 18.2 - - + -
205A GLN 3.4 25.6 - - - +
206A THR* 4.2 2.9 - - - -
217A ILE* 3.9 23.1 - - + -
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Residues in contact with MET 124 (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 PRO* 2.9 31.1 + - + +
121A ARG* 4.0 11.2 - - + +
123A VAL* 1.3 73.5 - - - +
125A ALA* 1.3 59.4 + - - +
127A MET* 3.3 4.0 + - - +
128A THR* 2.9 33.6 + - - -
217A ILE* 3.7 20.4 - - + -
221A GLU* 3.6 54.7 - - + +
222A LEU* 3.9 11.0 - - + +
225A TYR* 3.7 37.2 - - + -
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Residues in contact with ALA 125 (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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109A THR* 3.7 30.0 - - - +
112A ASP* 3.9 4.3 - - + -
113A LEU* 3.8 13.8 - - + +
121A ARG 2.9 19.6 + - - +
122A LYS 3.2 6.3 + - - +
124A MET* 1.3 77.1 - - - +
126A LEU* 1.3 56.9 + - - +
128A THR* 3.3 3.9 + - - -
129A ARG* 2.9 28.8 + - - +
225A TYR* 3.5 20.8 - - - +
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Residues in contact with LEU 126 (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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113A LEU* 3.6 19.7 - - + -
118A LEU* 4.6 9.2 - - + -
122A LYS* 2.9 24.4 + - + +
123A VAL* 3.4 15.7 - - + +
125A ALA* 1.3 76.2 - - - +
127A MET* 1.3 59.5 + - + +
129A ARG* 3.3 6.6 + - + +
130A LEU* 3.0 33.4 + - + +
187A THR* 4.4 8.1 - - + +
188A LEU* 3.8 23.4 - - + +
191A ASN* 3.6 41.5 - - + +
195A LEU* 4.6 13.2 - - + -
204A PHE* 5.4 6.7 - - + -
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Residues in contact with MET 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 2.9 23.7 + - - +
124A MET* 3.6 6.5 - - - +
126A LEU* 1.3 77.2 - - - +
128A THR* 1.3 56.4 + - - +
130A LEU* 3.2 5.9 + - - +
131A LEU* 3.0 25.8 + - - +
152A LEU* 3.3 22.0 - - + +
153A SER* 3.9 27.4 - - - +
204A PHE* 3.6 49.1 - - + -
217A ILE* 3.7 31.9 - - + +
222A LEU* 3.9 24.5 - - + -
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Residues in contact with THR 128 (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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105A LEU* 4.0 21.1 - - + -
109A THR* 4.3 2.7 - - + -
124A MET 2.9 22.6 + - - -
125A ALA* 3.7 5.8 - - - -
127A MET* 1.3 72.1 - - - +
129A ARG* 1.3 67.1 + - - +
131A LEU* 3.2 10.6 + - - +
132A HIS* 3.0 21.5 + - - +
222A LEU* 3.9 3.5 - - - +
225A TYR* 3.4 18.1 - - + -
226A LEU* 3.5 28.1 - - + +
238A PHE* 3.9 15.2 - - + -
804A ACY 4.2 6.1 - - + -
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LYS* 3.3 21.4 - - - +
109A THR* 4.9 1.2 + - - -
110A THR* 4.2 2.6 + - - -
113A LEU* 3.4 20.0 - - + +
125A ALA 2.9 13.4 + - - +
126A LEU* 3.3 10.5 + - - +
128A THR* 1.3 77.6 - - - +
130A LEU* 1.3 57.7 + - - +
132A HIS* 3.2 1.6 + - - +
133A VAL* 2.9 37.4 + - + +
185A ASP* 2.9 35.2 + - - -
187A THR* 3.7 8.9 - - - +
188A LEU* 3.9 23.1 - - + -
804A ACY 2.8 36.5 + - - +
11D C 2.9 43.0 + - - -
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Residues in contact with LEU 130 (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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126A LEU* 3.0 20.2 + - + +
127A MET* 3.2 8.0 + - - +
129A ARG* 1.3 77.7 - - - +
131A LEU* 1.3 56.5 + - - +
133A VAL* 4.4 2.0 - - - -
134A ALA* 2.9 31.9 + - - +
135A ARG 3.4 1.7 + - - -
136A PHE* 3.6 17.5 - - + -
152A LEU* 4.0 8.7 - - + -
167A VAL* 5.9 0.4 - - + -
169A PHE* 3.9 25.4 - - + -
183A THR* 3.8 28.7 - - + +
188A LEU* 3.8 19.5 - - + -
192A MET* 4.3 6.7 - - + -
204A PHE* 3.6 35.4 - - + -
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Residues in contact with LEU 131 (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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127A MET 3.0 18.4 + - - +
128A THR* 3.2 13.7 + - - +
130A LEU* 1.3 74.8 - - - +
132A HIS* 1.3 59.8 + - - +
135A ARG* 3.0 24.4 + - - +
136A PHE* 3.3 32.0 - - + +
137A ARG 4.3 1.1 - - - -
138A VAL* 3.9 24.9 - - + -
152A LEU* 3.9 16.2 - - + -
222A LEU* 4.4 7.6 - - + -
226A LEU* 3.7 31.2 - - + -
235A ALA* 4.3 3.6 - - + +
238A PHE* 3.5 35.3 - - + +
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Residues in contact with HIS 132 (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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102A LEU* 4.1 20.3 - - + +
106A LYS* 4.7 12.6 - - + -
128A THR 3.0 13.4 + - - +
129A ARG 3.5 7.0 - - - +
131A LEU* 1.3 80.4 - - - +
133A VAL* 1.3 67.6 + - + +
135A ARG* 4.4 9.9 + - - +
238A PHE* 3.6 31.7 - + + +
241A TRP* 4.6 9.2 - + - -
242A GLY* 5.2 3.6 - - - -
320A GLY 5.6 1.1 - - - -
322A THR* 5.8 2.9 - - + -
325A GLU* 2.7 37.2 + - - -
804A ACY 2.7 30.5 + - + +
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Residues in contact with VAL 133 (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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129A ARG* 2.9 37.9 + - + +
130A LEU* 4.4 1.6 - - - -
132A HIS* 1.3 89.4 - - + +
134A ALA* 1.3 60.1 + - - +
135A ARG* 3.3 19.5 + - - +
182A ALA 5.2 3.3 - - - +
183A THR* 3.8 26.9 - - + -
185A ASP* 6.0 2.5 - - + -
188A LEU* 4.2 12.3 - - + -
804A ACY 4.2 1.6 - - - +
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Residues in contact with ALA 134 (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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130A LEU 2.9 13.9 + - - +
133A VAL* 1.3 79.3 - - - +
135A ARG* 1.3 78.8 + - - +
136A PHE* 3.3 21.0 + - + -
181A LYS* 3.1 31.8 + - + +
182A ALA 4.7 4.3 - - - +
183A THR* 4.2 20.9 - - + -
277A ASP* 5.1 0.3 - - - +
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Residues in contact with ARG 135 (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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130A LEU 3.4 0.8 + - - -
131A LEU 3.0 14.7 + - - -
132A HIS 4.4 6.9 + - - +
133A VAL* 3.3 25.1 + - - +
134A ALA* 1.3 83.3 + - - +
136A PHE* 1.3 63.1 + - - +
181A LYS* 3.6 5.1 + - - -
238A PHE 4.0 6.5 - - - +
239A ARG* 2.9 34.2 + - + +
242A GLY* 3.4 44.6 + - - -
243A GLY* 3.8 3.4 - - - +
245A LEU* 5.7 6.1 - - - +
246A LEU* 4.1 24.3 - - - +
249A GLU* 5.9 0.2 + - - -
277A ASP* 2.9 41.8 + - - +
278A LEU* 4.0 14.6 - - + -
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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