Contacts of the helix formed by residues 125 - 140 (chain A) in PDB entry 3LL8
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 PHE 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.8 16.4 - - + -
93A GLY 3.0 19.2 + - - +
94A GLN* 5.1 1.8 - - - -
95A PHE* 3.5 16.4 - - + -
96A PHE* 3.9 29.2 - + - -
124A TYR* 1.3 90.2 - - + +
126A SER* 1.3 64.2 + - - +
128A GLU* 3.0 29.1 - - + +
129A CYS* 3.1 23.6 + - - -
169A LYS* 4.0 4.0 - - - -
339A HIS* 3.9 24.7 - + + -
340A PRO* 3.5 30.5 - - + -
342A TRP* 3.6 25.8 - + - -
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY* 3.5 11.4 - - - -
119A TYR 4.5 0.7 - - - -
120A VAL* 3.4 12.3 - - - +
121A ASP* 2.9 24.3 + - - -
123A GLY 3.3 13.2 + - - -
125A PHE* 1.3 78.4 - - - +
127A ILE* 1.3 57.4 + - - +
129A CYS* 3.3 4.1 + - - +
130A VAL* 3.0 30.5 + - - +
161A THR* 5.0 0.5 + - - -
162A PHE* 3.5 21.3 - - - +
165A GLU* 2.9 17.6 + - - -
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Residues in contact with ILE 127 (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 SER* 1.3 77.9 - - - +
128A GLU* 1.3 69.2 + - + +
130A VAL* 3.7 4.6 - - + +
131A LEU* 2.7 54.2 + - + +
162A PHE* 3.9 26.4 - - + -
165A GLU* 2.9 23.1 + - + +
166A CYS* 4.0 6.3 - - - -
169A LYS* 3.9 14.8 - - + -
170A TYR* 4.0 31.4 - - + -
174A VAL* 3.9 23.6 - - + -
178A CYS* 4.1 9.0 - - - -
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Residues in contact with GLU 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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50A LEU* 3.9 38.3 - - + +
53A GLU* 5.2 7.8 - - - +
54A GLY 4.9 8.0 - - - +
55A ARG* 6.1 0.5 - - - +
95A PHE* 3.4 25.4 - - + -
125A PHE* 3.0 29.6 - - + +
127A ILE* 1.3 80.5 - - + +
129A CYS* 1.3 64.0 + - - +
131A LEU* 4.5 2.9 - - + -
132A TYR* 2.9 27.5 + - - +
165A GLU* 3.3 1.0 - - - +
169A LYS* 2.9 38.3 + - - +
170A TYR* 6.0 1.5 - - + +
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Residues in contact with CYS 129 (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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91A ILE* 3.9 17.9 - - + -
93A GLY* 3.8 14.1 - - - -
95A PHE* 3.5 36.7 - - - -
98A LEU* 4.2 11.2 - - + -
119A TYR* 4.1 12.8 - - + +
125A PHE 3.1 19.1 + - - -
126A SER 3.3 7.6 + - - +
128A GLU* 1.3 77.0 - - - +
130A VAL* 1.3 56.6 + - - +
132A TYR* 3.8 0.7 - - - +
133A LEU* 3.0 41.8 + - + +
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Residues in contact with VAL 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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65A ILE* 4.8 8.5 - - + -
119A TYR* 4.7 7.0 - - + -
120A VAL* 3.5 25.8 - - + -
126A SER 3.0 20.6 + - - +
127A ILE* 3.7 8.5 - - + +
129A CYS* 1.3 72.9 - - - +
131A LEU* 1.3 69.7 + - - +
133A LEU* 4.9 1.3 - - - -
134A TRP* 2.9 52.1 + - + +
162A PHE* 4.3 6.1 - - + -
178A CYS* 4.3 20.0 - - - -
182A PHE* 3.9 15.9 - - + -
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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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46A LEU* 4.3 3.2 - - + +
50A LEU* 4.4 13.7 - - + -
56A LEU* 4.0 15.7 - - + -
61A ALA* 4.1 31.2 - - + +
64A ILE* 3.7 21.2 - - + +
65A ILE* 4.1 18.2 - - + -
127A ILE* 2.7 43.5 + - + +
128A GLU* 3.9 6.5 - - + +
130A VAL* 1.3 71.8 - - - +
132A TYR* 1.3 58.1 + - - +
135A ALA* 2.9 30.7 + - - +
170A TYR* 3.9 24.7 - - + +
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Residues in contact with TYR 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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43A VAL* 3.6 36.3 + - + +
46A LEU* 4.1 17.7 - - + -
47A LYS* 3.8 34.4 - - + +
50A LEU* 4.5 3.0 - - + +
95A PHE* 3.7 15.0 - + + -
98A LEU* 4.3 3.4 - - + -
99A MET* 3.7 20.8 - - + -
102A PHE* 3.8 21.1 - + - +
108A PRO* 5.7 2.3 - - - +
128A GLU 2.9 19.5 + - - +
129A CYS* 3.8 2.9 - - - +
131A LEU* 1.3 76.5 - - - +
133A LEU* 1.3 58.7 + - - +
135A ALA* 3.2 3.5 + - - +
136A LEU* 2.9 62.0 + - + +
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Residues in contact with LEU 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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91A ILE* 5.3 2.0 - - + -
98A LEU* 4.3 13.9 - - + -
102A PHE* 3.9 19.1 - - + -
115A PHE* 3.9 37.2 - - + -
119A TYR* 3.7 38.6 - - + -
129A CYS* 3.0 29.5 + - + +
130A VAL* 5.2 0.7 - - - -
132A TYR* 1.3 72.3 - - - +
134A TRP* 1.3 69.4 + - + +
136A LEU* 3.3 7.2 + - + +
137A LYS* 2.9 28.8 + - - +
144A LEU* 4.2 6.5 - - + +
146A LEU* 4.2 11.1 - - + +
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Residues in contact with TRP 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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64A ILE* 3.6 20.6 - - + +
65A ILE* 3.4 32.0 + - + +
68A GLY* 3.6 16.1 - - - -
69A ALA 3.9 5.9 - - - +
72A LEU* 3.7 21.8 - - + +
119A TYR* 4.5 15.3 - + - -
130A VAL* 2.9 42.7 + - + +
133A LEU* 1.3 84.3 - - + +
135A ALA* 1.3 61.9 + - - +
137A LYS* 3.2 7.4 + - + +
138A ILE* 3.0 27.9 + - - +
146A LEU* 3.8 20.0 - - + -
181A ALA* 3.6 16.1 - - + +
182A PHE* 3.7 36.1 - + - -
185A LEU* 4.0 18.4 - - + -
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Residues in contact with ALA 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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41A PRO* 3.4 23.6 - - + +
43A VAL* 4.2 11.0 - - + -
46A LEU* 3.5 25.8 - - + -
64A ILE* 3.8 12.4 - - + +
131A LEU 2.9 17.9 + - - +
132A TYR 3.4 4.9 - - - +
134A TRP* 1.3 77.1 - - - +
136A LEU* 1.3 56.6 + - - +
138A ILE* 3.3 4.5 + - - +
139A LEU* 3.0 23.9 + - - +
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Residues in contact with LEU 136 (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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43A VAL* 4.0 23.3 - - + -
102A PHE* 3.6 26.7 - - + -
108A PRO* 4.1 12.1 - - + -
132A TYR* 2.9 53.4 + - + +
133A LEU* 3.6 7.9 - - - +
135A ALA* 1.3 76.8 - - - +
137A LYS* 1.3 51.8 + - - +
139A LEU* 3.3 2.0 + - - -
140A TYR* 2.8 63.6 + - + +
144A LEU* 3.7 19.2 - - + +
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Residues in contact with LYS 137 (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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68A GLY* 4.9 6.1 - - - +
71A ILE* 3.9 26.9 - - + +
72A LEU* 4.0 18.6 - - + -
75A GLU* 2.9 37.7 + - - -
133A LEU 2.9 16.9 + - - +
134A TRP* 3.2 12.5 + - + +
136A LEU* 1.3 71.8 - - - +
138A ILE* 1.3 64.4 + - - +
140A TYR 4.6 1.3 - - - -
141A PRO* 3.1 42.6 + - + +
144A LEU* 2.7 38.4 + - + +
145A PHE* 3.7 8.1 - - - +
146A LEU* 4.4 8.7 - - + +
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Residues in contact with ILE 138 (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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35A PHE* 4.5 8.3 - - + -
39A GLY 4.5 6.1 - - - +
40A LYS* 5.6 0.2 - - - -
41A PRO* 3.9 17.7 - - + +
64A ILE* 3.6 37.7 - - + +
67A GLU* 3.6 31.9 - - + +
68A GLY* 3.8 14.1 - - - +
71A ILE* 3.6 18.6 - - + +
134A TRP 3.0 18.9 + - - +
135A ALA* 3.3 8.9 + - - +
137A LYS* 1.3 74.7 - - - +
139A LEU* 1.3 62.3 + - - +
141A PRO* 3.2 12.8 - - - +
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Residues in contact with LEU 139 (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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40A LYS* 3.9 50.3 + - + +
41A PRO* 4.0 15.5 - - + +
43A VAL* 3.6 32.1 - - + -
135A ALA 3.0 15.9 + - - +
136A LEU* 3.8 4.0 - - - +
137A LYS 3.3 0.4 - - - -
138A ILE* 1.3 78.4 - - - +
140A TYR* 1.3 95.8 + - + +
141A PRO* 3.3 7.0 - - - +
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Residues in contact with TYR 140 (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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43A VAL* 5.2 3.1 - - + +
108A PRO* 3.8 34.1 - - + +
109A ALA* 3.5 36.3 + - - +
136A LEU* 2.8 32.9 + - + +
137A LYS 3.5 3.4 - - - +
139A LEU* 1.3 108.5 - - + +
141A PRO* 1.4 62.8 - - - +
142A LYS 3.0 5.3 + - - -
143A THR* 3.2 24.9 + - - +
144A LEU* 3.2 19.8 + - + +
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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