Contacts of the strand formed by residues 135 - 144 (chain A) in PDB entry 1F5J
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 ALA 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.9 26.9 - - + -
125A ARG 4.0 0.5 - - - +
127A ASN* 3.1 6.4 + - - +
128A GLN 2.8 30.8 + - - +
130A SER* 3.9 3.1 - - - +
132A VAL* 4.8 4.3 - - + -
133A GLY 3.5 8.5 - - - +
134A THR* 1.3 79.8 - - - +
136A THR* 1.3 64.1 + - - +
137A PHE* 3.5 9.3 - - + -
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Residues in contact with THR 136 (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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88A LEU* 4.8 3.3 - - - +
124A THR* 4.6 8.5 - - + -
125A ARG 3.2 14.1 - - - +
126A VAL* 3.6 19.5 - - + +
127A ASN* 3.0 26.0 + - - -
135A ALA* 1.3 73.7 - - - +
137A PHE* 1.3 67.0 + - - +
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Residues in contact with PHE 137 (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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83A TRP* 3.6 30.5 - + - -
88A LEU* 3.3 37.2 - - + +
90A GLU* 3.7 18.6 - - + -
124A THR* 3.6 2.8 - - - +
125A ARG* 2.8 59.0 + - + +
128A GLN* 4.0 5.6 - - + -
129A PRO 3.6 20.2 - - - -
130A SER* 3.8 9.9 - - - -
135A ALA* 3.5 20.4 - - + -
136A THR* 1.3 81.3 - - - +
138A ASP* 1.3 76.3 + - - +
139A GLN* 4.4 0.2 - - + -
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Residues in contact with ASP 138 (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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88A LEU 4.1 3.8 + - - -
89A VAL* 3.5 11.3 - - + +
90A GLU 3.2 19.9 + - - -
122A ARG* 2.9 33.0 + - - +
123A THR 3.2 6.7 - - - +
124A THR* 2.7 31.5 + - - +
137A PHE* 1.3 81.8 - - - +
139A GLN* 1.3 63.2 + - - +
140A TYR* 4.1 22.8 + - + -
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Residues in contact with GLN 139 (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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90A GLU* 2.6 43.4 + - + +
92A TYR* 3.7 15.8 + - + -
122A ARG* 3.4 2.4 - - - -
123A THR* 2.6 58.5 + - - +
125A ARG* 3.1 42.5 - - + +
137A PHE* 4.4 0.4 - - + -
138A ASP* 1.3 76.5 - - - +
140A TYR* 1.3 70.2 + - - +
141A TRP* 3.5 23.5 - - + +
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Residues in contact with TYR 140 (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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87A PRO* 4.7 1.6 - - - +
89A VAL* 3.7 23.6 - - + +
90A GLU 3.1 6.3 + - - -
91A PHE* 3.3 3.9 - - + +
92A TYR* 2.8 26.9 + - - +
121A TYR 3.5 2.7 - - - -
122A ARG* 4.4 4.3 - - + -
138A ASP* 4.1 23.7 + - + -
139A GLN* 1.3 81.1 - - - +
141A TRP* 1.3 63.4 + - - +
162A TRP* 3.9 28.0 - + + -
167A LEU* 3.6 50.3 - - + -
168A ASN* 2.8 40.6 + - - -
169A LEU* 3.7 21.1 - - + -
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Residues in contact with TRP 141 (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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77A TYR* 3.9 23.3 - + - -
92A TYR* 3.4 57.9 - + + -
94A VAL* 3.9 12.1 - - + -
102A PRO* 3.9 15.5 - - + -
103A PRO* 3.4 29.8 - - + -
120A ILE* 3.2 6.6 - - - +
121A TYR* 2.8 54.1 + - + +
123A THR* 2.9 24.7 + - + +
139A GLN* 3.5 27.5 - - - +
140A TYR* 1.3 80.5 - - - +
142A SER* 1.3 59.2 + - - +
143A VAL* 4.1 11.9 - - + -
162A TRP* 3.6 10.4 + - - -
167A LEU* 5.2 0.2 - - - +
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Residues in contact with SER 142 (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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92A TYR 3.1 9.6 + - - +
93A ILE* 3.4 3.4 - - - -
94A VAL* 2.8 27.0 + - - +
111A VAL* 5.3 0.9 - - - +
118A TYR* 4.0 9.5 - - - +
119A ASP 3.3 6.5 - - - -
120A ILE* 4.2 7.6 - - - +
141A TRP* 1.3 70.5 - - - +
143A VAL* 1.3 61.7 + - - +
158A HIS* 2.8 36.2 + - - -
161A ALA* 5.7 0.2 - - - +
162A TRP* 2.8 26.2 + - - -
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Residues in contact with VAL 143 (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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94A VAL* 3.9 27.8 - - + -
97A TRP* 4.4 1.6 - - + -
101A ARG* 2.9 47.4 + - + +
102A PRO* 3.5 32.8 - - + +
103A PRO* 4.1 2.2 - - + -
118A TYR* 3.6 3.7 - - - -
119A ASP 2.9 23.0 + - - -
121A TYR* 3.8 24.0 - - + -
141A TRP* 4.1 9.0 - - + -
142A SER* 1.3 79.0 - - - +
144A ARG* 1.3 64.6 + - - +
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Residues in contact with ARG 144 (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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94A VAL 3.1 20.0 + - - +
95A GLU* 4.1 10.8 - - - +
97A TRP* 3.2 11.6 - - + -
101A ARG* 3.0 17.7 + - - -
116A GLY* 4.0 21.4 - - - +
117A THR 3.3 14.1 - - - +
118A TYR* 3.3 29.4 + - + -
143A VAL* 1.3 71.5 - - - +
145A THR* 1.3 64.3 + - - +
146A SER* 2.9 51.4 + - - +
147A LYS 4.0 3.0 + - - -
148A ARG* 3.7 48.4 - - - +
59B LEU 5.6 1.6 + - - -
197B GLN* 4.2 17.2 + - - +
198B SER* 4.5 2.6 - - - +
199B SER* 4.2 15.8 - - - +
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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