Contacts of the strand formed by residues 119 - 130 (chain A) in PDB entry 4LL1
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 GLY 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LYS 3.5 6.3 - - - -
54A VAL* 4.5 4.0 - - - -
114A PHE* 3.0 29.5 + - - +
115A LYS* 3.6 6.1 - - - -
116A GLY* 2.8 29.3 + - - +
118A TYR* 1.3 80.9 - - - +
120A SER* 1.3 64.1 + - - -
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A VAL 4.0 0.6 - - - +
52A ALA* 3.2 6.8 - - - +
53A LYS* 2.9 60.3 + - - +
111A GLY 5.4 0.2 - - - -
114A PHE 3.9 3.6 + - - +
115A LYS* 5.0 3.4 - - - +
118A TYR 5.2 0.3 + - - -
119A GLY* 1.3 75.9 - - - -
121A VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 121 (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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51A VAL 3.6 7.6 - - - +
52A ALA* 4.5 3.1 - - + -
110A LEU 4.0 6.3 - - - +
111A GLY 3.9 22.7 - - - +
112A THR* 4.5 13.5 - - - +
114A PHE 6.0 0.2 - - - +
115A LYS* 5.8 7.3 - - + +
120A SER* 1.3 76.5 - - - +
122A ASP* 1.3 69.5 + - - +
123A TYR* 3.7 27.1 - - + +
145A VAL* 4.6 10.8 - - + +
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Residues in contact with ASP 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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49A CYS 3.5 1.7 - - - +
50A GLY* 3.1 5.7 - - - -
51A VAL* 2.9 42.5 + - + +
121A VAL* 1.3 81.0 - - - +
123A TYR* 1.3 61.1 + - - +
124A TRP* 3.7 18.2 + - - +
140A LYS* 5.4 1.8 + - - -
142A ASN* 3.4 22.1 + - - +
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Residues in contact with TYR 123 (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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49A CYS 3.2 2.2 - - - -
50A GLY* 3.6 23.8 - - - -
51A VAL 4.4 0.2 - - - -
69A TYR* 3.4 19.1 - - - +
70A LEU* 4.0 9.0 - - + -
105A LEU* 3.7 20.2 - - + -
106A PRO* 5.3 0.4 - - + +
110A LEU* 2.7 38.7 + - + +
121A VAL* 3.7 20.2 - - + +
122A ASP* 1.3 88.3 + - - +
124A TRP* 1.3 60.4 + - - +
142A ASN* 3.2 9.6 + - - +
143A PHE* 2.8 75.7 + + + +
145A VAL* 3.9 22.4 - - + -
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Residues in contact with TRP 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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47A LEU* 3.7 24.0 - - + -
48A ALA* 3.2 4.0 - - - +
49A CYS* 2.8 65.7 + - + +
51A VAL* 5.9 4.7 - - + +
122A ASP* 3.7 31.3 + - - +
123A TYR* 1.3 76.1 - - - +
125A VAL* 1.3 62.8 + - - +
126A LYS* 3.1 53.4 - - + -
140A LYS* 3.5 34.1 - - + +
141A LYS 3.5 14.4 - - - +
142A ASN* 3.8 10.1 - - - +
143A PHE* 3.8 5.9 - - - -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.2 21.8 - - + +
14A PHE* 3.8 29.6 - - + -
46A ILE* 4.1 24.9 - - + -
47A LEU 3.4 7.0 - - - +
48A ALA* 4.3 1.6 - - + -
101A PHE* 4.5 4.0 - - + -
103A PHE* 4.1 21.5 - - + -
124A TRP* 1.3 81.9 - - - +
126A LYS* 1.3 74.2 + - - +
139A THR 3.9 0.5 - - - +
140A LYS* 3.3 1.9 - - - -
141A LYS 2.9 32.4 + - - +
143A PHE* 4.1 4.5 - - + -
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.2 5.4 - - - +
47A LEU* 2.8 39.9 + - - +
124A TRP* 3.1 43.3 - - + -
125A VAL* 1.3 76.0 - - - +
127A ALA* 1.3 58.7 + - - +
128A PHE* 3.7 23.7 - - + -
138A GLU* 2.8 29.8 - - + +
139A THR 3.1 7.4 - - - +
140A LYS* 3.9 31.6 - - + +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.6 18.7 - - + -
12A VAL* 4.1 8.8 - - + +
31A VAL* 3.9 23.6 - - + -
44A VAL* 5.1 0.4 - - + -
45A ARG 3.1 10.5 - - - +
46A ILE* 4.1 1.6 - - + -
125A VAL 4.1 0.6 + - - -
126A LYS* 1.3 73.2 - - - +
128A PHE* 1.3 61.4 + - - +
138A GLU* 3.3 7.3 - - - +
139A THR* 2.9 43.1 + - + +
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Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.6 3.6 - - - -
43A ALA 3.8 0.7 - - - +
44A VAL* 3.2 8.5 - - - +
45A ARG* 2.9 84.5 + - + +
46A ILE 4.3 0.9 - - - -
47A LEU* 3.6 37.0 - - + -
126A LYS* 3.7 26.2 - - + -
127A ALA* 1.3 75.4 - - - +
129A LEU* 1.3 60.1 + - - +
130A ASP* 4.1 2.0 + - - +
136A THR* 4.8 8.7 - - - +
137A GLN 3.4 6.3 - - - +
138A GLU* 3.7 34.5 - - + -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.9 42.0 - - + -
10A PHE* 3.5 20.5 - - + -
33A VAL* 4.5 13.5 - - + -
41A VAL* 3.7 29.2 - - + -
43A ALA 3.7 0.7 - - - -
44A VAL* 3.7 22.9 - - + -
91A MET* 5.1 0.2 - - + -
128A PHE* 1.3 71.4 - - - +
130A ASP* 1.3 61.4 + - - +
131A ARG* 4.0 16.0 + - + +
135A PRO 4.6 0.7 - - - +
136A THR* 3.4 4.9 - - - -
137A GLN* 2.7 44.9 + - + +
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Residues in contact with ASP 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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41A VAL* 3.8 2.9 - - - +
42A LYS* 2.9 36.6 + - + -
43A ALA* 2.9 29.8 + - + +
45A ARG* 2.6 48.1 + - - -
128A PHE* 4.4 1.3 - - - +
129A LEU* 1.3 74.6 - - - +
131A ARG* 1.3 64.7 + - - +
136A THR* 3.0 26.7 - - + +
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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