Contacts of the strand formed by residues 121 - 128 (chain B) in PDB entry 3L6D
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 HIS 121 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B HIS* 4.6 10.7 + - - -
95B ARG 2.9 19.3 + - - -
96B THR* 3.3 12.9 - - - +
97B ILE 2.9 26.0 + - - +
115B VAL* 3.5 6.1 - - - +
116B ASN* 4.1 3.5 + - - +
119B GLY 4.3 8.8 + - - -
120B GLY* 1.3 83.7 + - - -
122B TYR* 1.3 60.6 + - - +
123B VAL 4.1 0.2 - - - -
146B ASP* 3.5 18.1 + - - +
149B ALA* 3.5 27.8 - - + +
152B GLN* 5.5 4.5 - - - -
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Residues in contact with TYR 122 (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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79B THR* 6.2 0.2 - - + -
97B ILE* 3.7 11.0 - - + -
99B ASP* 2.6 46.4 + - + +
103B ASN* 5.4 0.7 + - - -
108B GLY* 4.1 9.0 - - - -
111B LEU* 4.0 22.7 - - + +
112B GLN* 3.7 42.8 + - + +
115B VAL* 4.0 26.2 - - + -
116B ASN* 4.0 5.4 - - - +
121B HIS* 1.3 73.6 - - - +
123B VAL* 1.3 63.7 + - - +
124B LYS* 3.9 30.0 + - + +
145B GLY* 3.7 1.3 - - - -
146B ASP* 3.0 27.5 + - - +
169B TRP* 4.0 15.0 - + - -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B THR* 3.9 18.2 - - + -
97B ILE 2.8 15.4 + - - +
98B VAL* 3.2 12.0 - - + -
99B ASP* 2.7 33.6 + - - +
122B TYR* 1.3 80.7 - - - +
124B LYS* 1.3 63.8 + - - +
143B HIS* 3.9 25.6 - - + -
144B THR 3.4 11.9 - - - +
146B ASP 3.8 9.2 - - - +
149B ALA* 4.1 2.9 - - + -
150B PHE* 3.8 35.2 - - + +
157B LEU* 5.0 1.6 - - + -
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Residues in contact with LYS 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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99B ASP* 3.5 10.6 + - - +
101B THR 4.1 8.7 + - - -
102B THR* 5.4 0.8 - - - +
103B ASN* 3.5 37.0 + - - +
122B TYR* 3.9 25.2 + - + +
123B VAL* 1.3 74.9 - - - +
125B GLY* 1.3 66.7 + - - +
126B MSE 4.1 17.3 - - + +
142B ILE 4.0 0.2 - - - +
143B HIS* 3.2 4.7 - - - -
144B THR* 2.9 51.1 + - + +
169B TRP* 4.0 19.7 - - + -
173B LEU* 3.8 24.7 - - + -
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Residues in contact with GLY 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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98B VAL* 4.9 0.2 - - - +
99B ASP 2.8 20.4 + - - +
100B TYR* 3.5 29.5 - - - +
123B VAL 3.9 0.8 + - - -
124B LYS* 1.3 78.5 + - - +
126B MSE 1.3 68.4 - - - +
142B ILE 3.5 5.8 - - - -
143B HIS* 3.5 15.9 - - - -
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Residues in contact with MSE 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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100B TYR* 3.9 2.3 - - - -
124B LYS* 4.1 23.6 - - + +
125B GLY* 1.3 82.7 - - - +
127B ILE* 1.3 62.1 + - - +
128B VAL* 3.6 4.2 + - - +
141B SER* 3.3 3.3 - - - -
142B ILE* 2.9 70.1 + - + +
143B HIS* 4.4 1.3 - - - -
144B THR* 4.5 2.9 - - + -
172B ALA* 3.5 42.0 - - + +
173B LEU* 3.9 19.5 - - + -
176B ALA* 4.1 16.8 - - + -
180B HIS* 5.5 6.3 - - + -
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Residues in contact with ILE 127 (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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20B MSE 4.1 24.5 - - + -
24B MSE 4.1 17.9 - - + -
100B TYR* 4.4 14.6 - - + -
126B MSE 1.3 72.3 - - - +
128B VAL* 1.3 61.5 + - - +
129B ALA* 2.9 26.1 + - + +
134B VAL* 4.2 16.6 - - + -
139B SER* 5.4 0.2 - - - -
140B HIS 4.0 6.3 - - - +
141B SER* 4.2 4.9 - - - -
160B LEU* 3.6 33.4 - - + +
161B ALA* 3.9 12.1 - - + -
180B HIS* 4.9 4.9 + - - -
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Residues in contact with VAL 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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214A THR* 4.3 11.4 - - + +
215A SER* 5.5 0.7 - - - -
217A PHE* 6.2 0.3 - - - -
218A PHE* 3.4 39.3 - - + +
126B MSE 4.0 8.3 - - - +
127B ILE* 1.3 70.9 - - - +
129B ALA* 1.3 60.1 + - - +
139B SER* 4.9 1.0 + - - -
140B HIS* 2.8 36.3 + - + +
141B SER* 4.5 2.0 - - - -
142B ILE* 4.5 8.1 - - + -
179B LEU* 3.9 32.1 - - + -
180B HIS* 4.1 22.2 - - + +
183B ALA* 6.0 0.4 - - + -
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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
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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