Contacts of the strand formed by residues 109 - 121 (chain B) in PDB entry 3M4D
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 THR 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B ILE* 4.0 8.5 - - + +
108B ASP* 1.3 84.3 - - - +
110B LYS* 1.3 69.7 + - - +
148B TYR* 4.0 10.6 - - - +
149B VAL 5.2 1.4 + - - +
149C VAL* 4.2 18.9 - - + +
150C GLN 3.7 6.3 - - - -
151C PRO* 3.7 23.8 - - + -
152C ASP* 5.1 0.2 - - - -
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Residues in contact with LYS 110 (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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109B THR* 1.3 80.9 - - - +
111B GLU* 1.3 59.8 + - - +
146B LEU* 3.7 22.9 - - + -
147B LYS 3.3 14.6 - - - +
148B TYR* 3.7 12.1 - - + +
149C VAL* 3.6 4.6 - - - +
150C GLN* 2.8 48.9 + - - +
151C PRO 3.7 0.2 - - - -
152C ASP* 2.6 30.8 + - - +
173C ASN* 2.6 41.1 + - - -
174C MET* 4.4 3.1 - - - +
175C VAL* 4.2 8.3 - - + -
181C PRO* 4.0 15.5 - - + -
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Residues in contact with GLU 111 (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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110B LYS* 1.3 73.8 - - - +
112B TYR* 1.3 63.4 + - - +
113B ASN* 3.2 28.7 + - - +
145B THR 3.7 0.8 - - - +
146B LEU* 3.4 8.5 - - - +
147B LYS* 2.7 63.7 + - + +
147C LYS* 4.0 15.6 + - + +
148C TYR 3.4 14.4 - - - +
149C VAL* 4.4 13.2 - - + +
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Residues in contact with TYR 112 (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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110B LYS 4.1 0.2 + - - -
111B GLU* 1.3 75.4 - - - +
113B ASN* 1.3 77.2 + - - +
114B SER* 3.0 26.9 - - - -
144B HIS* 2.8 38.9 + + + +
145B THR 3.4 7.4 - - - -
146B LEU* 5.3 5.2 - - + -
146C LEU* 3.7 0.9 - - + +
147C LYS* 3.6 0.3 - - - -
148C TYR* 2.7 30.9 + - + +
150C GLN* 3.6 27.8 - - - +
180C GLY 4.4 5.6 - - - -
181C PRO* 3.7 31.2 - - + -
178D ASN* 3.8 30.3 + - - +
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Residues in contact with ASN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLU* 3.2 33.2 + - - +
112B TYR* 1.3 103.0 + - - +
114B SER* 1.3 61.9 + - - +
115B THR* 5.0 2.2 - - - +
143B GLY 3.9 0.2 - - - +
144B HIS* 3.1 6.6 - - - -
145B THR* 2.8 50.3 + - - +
147B LYS* 4.1 16.3 + - - -
145C THR* 4.7 7.0 - - + -
146C LEU 3.1 6.5 - - - +
147C LYS* 3.5 30.8 - - + +
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Residues in contact with SER 114 (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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112B TYR* 3.0 25.9 - - - -
113B ASN* 1.3 70.5 - - - +
115B THR* 1.3 63.6 + - - +
143B GLY 3.5 4.9 - - - -
144B HIS* 3.1 15.5 + - - -
144C HIS 3.8 0.5 - - - +
145C THR* 3.2 3.3 - - - +
146C LEU* 2.8 42.3 + - - +
178D ASN* 3.6 22.8 + - - +
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Residues in contact with THR 115 (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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113B ASN* 5.0 3.1 - - - +
114B SER* 1.3 76.8 + - - +
116B LEU* 1.3 63.5 + - - +
117B THR* 3.8 17.9 - - - +
141B SER 3.7 1.0 - - - +
142B ILE* 3.3 8.2 - - - +
143B GLY* 2.8 44.6 + - - -
144B HIS* 5.4 0.2 - - - -
143C GLY* 5.5 0.7 - - - -
144C HIS 3.2 7.4 - - - +
145C THR* 2.9 32.4 + - - +
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Residues in contact with LEU 116 (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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115B THR* 1.3 73.5 - - - +
117B THR* 1.3 62.4 + - - +
118B TYR* 3.2 36.4 - - + +
140B VAL* 3.9 18.6 - - + -
141B SER 3.4 7.4 - - - +
142B ILE* 3.5 32.5 - - + -
142C ILE 3.9 0.9 - - - +
143C GLY* 3.4 1.2 - - - -
144C HIS* 3.0 42.8 + - + +
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Residues in contact with THR 117 (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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115B THR* 3.8 16.3 - - - +
116B LEU* 1.3 78.4 + - - +
118B TYR* 1.3 72.8 + - - +
139B ASN* 3.9 4.1 - - - +
140B VAL* 3.2 6.1 - - - +
141B SER* 2.9 51.0 + - - +
141C SER* 4.4 11.7 - - - -
142C ILE 3.4 17.0 - - - +
143C GLY* 4.1 4.6 - - - -
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Residues in contact with TYR 118 (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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116B LEU* 3.2 44.4 - - + +
117B THR* 1.3 79.4 - - - +
119B GLY* 1.3 59.0 + - - +
120B PHE* 5.3 15.0 - + + -
139B ASN* 3.4 6.5 - - - +
140B VAL* 3.8 29.5 - - + +
141C SER* 3.2 4.2 - - - -
142C ILE* 2.9 44.1 + - + +
144C HIS* 5.6 7.4 - + - -
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Residues in contact with GLY 119 (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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118B TYR* 1.3 76.6 - - - +
120B PHE* 1.3 75.1 + - - -
138B ALA* 3.6 0.2 - - - +
139B ASN* 2.8 48.7 + - - +
140C VAL 3.4 9.9 - - - -
141C SER* 3.7 10.1 - - - -
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Residues in contact with PHE 120 (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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118B TYR* 5.3 13.7 - + + -
119B GLY* 1.3 92.6 - - - -
121B ASN* 1.3 65.8 + - - +
137B GLY 3.5 5.8 - - - +
138B ALA* 3.5 20.9 - - + -
139B ASN* 4.4 1.3 - - - +
139C ASN* 3.4 2.1 - - - +
140C VAL* 3.0 40.6 + - + +
141C SER* 4.8 0.4 + - - -
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Residues in contact with ASN 121 (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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123A ASN* 5.3 1.8 + - - -
120B PHE* 1.3 79.2 - - - +
122B GLY* 1.3 65.7 + - - +
135B LEU* 3.8 11.0 - - - +
136B ILE* 3.5 4.4 - - - +
137B GLY* 2.9 45.4 + - - +
138B ALA 5.1 0.3 - - - -
139B ASN* 4.6 9.5 + - - +
138C ALA 3.3 16.2 - - - +
139C ASN* 3.7 11.0 - - + +
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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