Contacts of the strand formed by residues 128 - 138 (chain L) in PDB entry 1MHP
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 128 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148H LYS* 4.5 14.6 - - - -
123L GLN* 3.1 41.0 + - - +
124L LEU* 3.7 5.6 + - - -
126L SER* 3.5 6.2 + - - -
127L GLY* 1.3 83.9 + - - +
129L ALA* 1.3 66.5 - - - +
179L THR* 4.2 16.2 - - - +
180L LEU 4.0 8.3 - - - +
181L SER* 4.5 2.5 - - - +
182L LYS* 3.9 5.7 - - - +
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Residues in contact with ALA 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L PRO* 3.6 14.8 - - + -
123L GLN* 3.3 3.8 - - - -
124L LEU* 3.5 23.8 - - + -
128L THR* 1.3 75.3 - - - +
130L SER* 1.3 61.2 + - - +
179L THR* 3.5 2.6 + - - -
180L LEU* 2.8 46.8 + - + +
181L SER 4.7 0.9 - - - +
182L LYS 4.2 0.2 - - - +
185L TYR* 3.7 20.9 - - + -
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Residues in contact with SER 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H LEU* 3.6 26.3 - - - +
148H LYS* 3.7 23.6 + - - +
117L PHE 4.2 0.3 - - - +
118L PRO 4.1 1.0 - - - -
119L PRO* 3.2 23.3 - - - +
123L GLN* 2.7 26.6 + - - +
128L THR* 4.6 0.2 - - - +
129L ALA* 1.3 74.6 + - - +
131L VAL* 1.3 61.4 + - - +
132L VAL* 4.2 2.6 + - - +
177L THR* 4.3 12.6 - - - +
178L LEU 3.4 4.5 - - - -
179L THR* 4.4 6.0 + - - +
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Residues in contact with VAL 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L ILE* 4.3 2.0 - - + -
117L PHE 3.5 12.3 - - - +
119L PRO* 3.8 19.3 - - + -
130L SER* 1.3 75.3 - - - +
132L VAL* 1.3 61.7 + - - +
147L TRP* 3.4 30.6 - - + -
177L THR* 3.3 2.3 - - - -
178L LEU* 2.7 59.7 + - + +
180L LEU* 4.6 4.5 - - + -
185L TYR* 4.1 15.3 - - + -
191L TYR* 4.5 5.8 - - + -
208L PHE* 3.8 22.7 - - + -
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Residues in contact with VAL 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H LEU* 4.5 16.2 - - + -
146H LEU* 4.5 8.7 - - + -
171H PHE* 6.3 0.2 - - + -
184H SER* 4.3 19.5 - - - +
186H VAL* 5.9 2.5 - - + -
116L ILE* 3.4 2.1 - - - -
117L PHE* 2.7 62.2 + - + -
130L SER 4.2 1.1 - - - +
131L VAL* 1.3 77.5 - - - +
133L CYS* 1.3 72.9 + - - +
134L LEU* 4.8 2.5 - - + +
147L TRP* 4.2 2.9 - - - -
175L SER* 4.7 9.9 - - - -
176L SER 3.5 5.8 - - - +
177L THR* 3.6 27.8 - - + +
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Residues in contact with CYS 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L VAL* 5.3 1.8 - - - -
115L PHE 3.4 6.3 - - - -
116L ILE* 4.4 0.7 - - - +
132L VAL* 1.3 75.5 - - - +
134L LEU* 1.3 61.9 + - - +
135L LEU* 4.0 18.8 - - - +
145L VAL* 4.0 6.5 - - - -
147L TRP* 3.5 17.6 - - + -
174L LEU 4.0 0.3 - - - +
175L SER* 3.5 4.5 - - - -
176L SER* 2.8 36.6 + - - +
193L CYS* 2.0 49.1 - - - -
195L VAL* 4.4 6.5 - - - -
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Residues in contact with LEU 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H ALA* 4.2 6.5 - - + -
171H PHE* 3.4 34.5 - - + -
186H VAL* 3.3 32.1 - - + -
188H THR* 5.3 1.1 - - + -
113L SER 3.3 1.4 - - - +
114L VAL* 2.8 29.6 - - - +
115L PHE* 2.7 48.7 + - + +
117L PHE* 4.5 9.9 - - + -
132L VAL* 5.2 2.7 - - + -
133L CYS* 1.3 75.3 - - - +
135L LEU* 1.3 79.6 + - - +
136L ASN* 4.2 14.8 - - + +
174L LEU 3.6 2.2 - - - +
175L SER* 5.0 0.4 - - - -
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Residues in contact with LEU 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L PRO* 4.2 6.1 - - + -
113L SER 3.6 3.6 - - - -
114L VAL* 4.5 1.8 - - + +
133L CYS* 4.0 12.6 - - + -
134L LEU* 1.3 81.0 - - - +
136L ASN* 1.3 60.7 + - - +
138L PHE* 3.4 18.1 - - + -
143L ALA* 3.7 24.5 - - + -
144L LYS 4.9 0.2 - - - +
145L VAL* 3.4 36.1 - - + -
173L SER* 3.4 1.2 - - - -
174L LEU* 2.8 48.2 + - + +
195L VAL* 3.6 38.4 - - + -
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Residues in contact with ASN 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H HIS* 3.2 21.1 - - - -
186H VAL* 5.5 1.6 - - - +
188H THR* 3.7 24.2 + - - +
111L ALA 4.4 0.2 - - - +
112L PRO* 3.4 2.1 - - - +
113L SER* 2.9 41.2 + - - +
115L PHE* 4.0 13.8 - - + -
134L LEU* 4.2 14.5 - - + +
135L LEU* 1.3 74.1 - - - +
137L ASN* 1.3 91.2 + - - +
138L PHE* 3.6 4.3 - - - -
173L SER* 3.0 21.6 + - - -
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Residues in contact with ASN 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167H GLY* 6.3 0.8 - - - -
169H HIS* 3.0 28.0 + - - -
188H THR* 5.3 4.2 + - - -
110L ALA* 4.4 5.2 - - - +
111L ALA 3.8 9.7 - - - +
113L SER* 6.0 0.4 - - - +
136L ASN* 1.3 89.3 + - - +
138L PHE* 1.3 59.2 + - - +
169L ASP* 4.3 12.6 + - - +
171L THR* 3.3 30.5 + - + +
172L TYR 3.3 2.2 + - - -
173L SER* 3.2 7.8 + - - -
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Residues in contact with PHE 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L ALA* 3.1 17.9 - - - +
112L PRO* 3.3 34.1 - - + -
135L LEU* 3.4 26.0 - - + -
136L ASN 3.8 5.8 - - - -
137L ASN* 1.3 72.1 - - - +
139L TYR* 1.3 65.3 + - - +
140L PRO 3.2 20.0 - - - -
141L ARG 3.6 23.6 - - - -
143L ALA* 3.8 14.8 - - + -
162L VAL* 5.7 1.3 - - + -
171L THR* 3.1 6.3 - - - -
172L TYR* 2.8 67.1 + - + +
174L LEU* 3.5 26.2 - - + -
197L HIS* 3.4 9.6 - + - +
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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