Contacts of the strand formed by residues 137 - 143 (chain B) in PDB entry 1F1H
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 ASP 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A TYR 5.2 1.6 + - - -
167A GLY* 3.5 10.8 - - - -
168A ASN* 2.6 39.4 + - - +
135B PHE* 3.7 4.7 - - - +
136B ASP* 1.3 84.0 - - + +
138B ILE* 1.3 61.2 + - - +
139B ARG* 2.7 37.8 + - - +
150B ALA 4.7 1.0 - - - +
151B ILE* 3.7 1.7 - - - -
152B ASP* 2.9 48.1 + - + +
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Residues in contact with ILE 138 (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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160A SER 4.0 1.4 - - - +
168A ASN* 3.0 29.8 + - - +
169A LYS 3.6 19.5 - - - +
170A GLY* 3.7 10.9 - - - -
135B PHE* 4.8 4.5 - - + -
137B ASP* 1.3 75.7 - - - +
139B ARG* 1.3 65.2 + - - +
140B PHE* 4.0 17.2 - - + -
149B VAL* 4.3 5.2 - - + -
150B ALA 3.6 3.1 - - - +
151B ILE* 3.8 28.9 - - + -
252B THR* 4.2 1.8 - - + +
462H PHE* 4.1 17.7 - - + -
466H TYR* 3.5 46.9 - - + +
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Residues in contact with ARG 139 (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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160A SER 3.2 4.7 - - - +
161A SER* 3.9 14.2 + - - +
162A THR 3.5 25.4 - - - +
163A LYS* 3.8 39.6 - - - +
168A ASN* 3.7 6.5 - - + +
137B ASP* 2.7 41.3 + - - -
138B ILE* 1.3 79.0 - - - +
140B PHE* 1.3 64.5 + - - +
148B HIS* 4.3 10.4 + - - +
149B VAL* 3.2 2.8 - - - +
150B ALA* 2.7 63.3 + - + +
152B ASP* 5.5 2.4 - - - +
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Residues in contact with PHE 140 (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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160A SER* 2.8 60.0 + - - -
161A SER* 3.3 2.9 + - - -
170A GLY* 4.8 12.6 - - - -
172A ARG* 6.3 1.3 - - + -
138B ILE* 4.0 24.0 - - + -
139B ARG* 1.3 81.7 - - - +
141B GLY* 1.3 63.0 + - - +
148B HIS* 3.1 23.9 + - - +
149B VAL* 4.0 5.8 - - + -
459H PRO 4.4 2.9 - - - +
462H PHE* 3.6 38.1 - - + -
463H GLU* 3.5 36.6 - - + -
466H TYR* 4.3 12.8 - + + -
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Residues in contact with GLY 141 (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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160A SER* 4.3 3.4 - - - -
161A SER* 4.8 2.7 - - - -
140B PHE* 1.3 78.8 - - - +
142B ALA* 1.3 62.4 + - - +
147B SER* 3.2 4.0 - - - -
148B HIS* 2.9 42.9 + - - +
459H PRO* 4.2 4.8 + - - +
463H GLU* 4.2 12.1 - - - -
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Residues in contact with ALA 142 (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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141B GLY* 1.3 75.0 - - - +
143B SER* 1.3 61.3 + - - +
146B GLY 3.4 9.6 - - - +
147B SER* 4.2 6.5 - - - -
452B ARG* 4.4 5.7 + - - +
456B THR* 4.9 6.3 - - + -
460H VAL* 3.9 28.0 - - + -
463H GLU* 4.0 18.3 + - - +
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Residues in contact with SER 143 (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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142B ALA* 1.3 75.7 - - - +
144B ILE* 1.3 68.5 + - - +
145B SER* 3.2 20.6 + - - -
146B GLY 2.8 22.2 + - - +
261H PHE* 5.6 7.2 + - - +
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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